Secret Santa Exchange 2012: Intruder Part One
Title: Intruder
Author: stella_pegasi
Recipient: ArtisticAbandon
Word Count: ~16,800
Rating: PG
Warnings: Minor language, whump
Summary: There is an intruder on Atlantis, who may cost John Sheppard his life.
Author Notes: Many thanks to black_raven135 for being the beta for this story. As always, I appreciate her keen eye and insight.
By stella_pegasi
Part One
John Sheppard moved silently along the darkened passageway, trying to concentrate on the soothing resonance of the waves lapping at Atlantis’ hull. Night after night, he roamed unexplored sections of the city, trying to escape the sounds in his head.
Without thinking, he changed direction abruptly and exited the passageway onto the deck; the doors opening without a conscious thought. He sucked in salty fresh air, rubbing his temples as he exhaled. Nothing helped; the sounds remained. In the bright moonlight, he walked to the railing surrounding the open section of the hull nicknamed the canal, and peered over the side, gazing at the inflatable rafts special ops used to train divers. The small rafts bobbed up and down with the gentle waves.
Leaning his elbows on the railing, he cradled his pounding head, making a vain attempt to will away the pain. But the sensation wouldn’t go away; the nagging feeling that someone was calling his name, that someone was with him. An impression of urgency, yet when he tried to concentrate, he couldn’t quite grasp the thought.
Sheppard was exhausted, sleep elusive, hindered by the pain. People were beginning to notice; Weir asked him at the morning briefing if he was all right, while Lorne caught him napping in the middle of the afternoon. At dinner, Teyla’s telltale eyebrow arched when he told her he was fine; she clearly didn’t believe him. After dinner, when he heard Beckett was looking for him, he knew she’d tattled. He never cared for busybodies; he was just fine.
He scoffed, “Yeah, John, keep telling yourself that; you’re just fine.”
He blew out a deep breath, knowing he wasn’t fine and debating with himself about going to Beckett. He hadn’t quite convinced himself when a claxon blared, the loud, grating sound startling him as intense pain flooded his head. Grabbing his head, he lost his footing and slipped over the railing, landing in one of the inflatable rafts, unconscious.
~ooOoo~
Dr. Elizabeth Weir stood, arms crossed, glaring at Senior Gate Technician Lt. Chuck Campbell. “What do you mean you can’t find him? How can you possibly not know where Colonel Sheppard is?”
“Ma’am, he’s not in his quarters, and his team hasn’t seen him since dinner. Teyla and Ronon are tracing his normal running route to see if he decided to go for a run.”
She sighed, “He couldn’t…” the claxon blared again, interrupting her. Through gritted teeth, she said, “Can you turn that thing off?”
Chuck quickly pressed a series of crystals on the control panel, “Sorry, Dr. Weir, I thought I had turned it off.”
“As I was saying, Sheppard didn’t just vanish, get Lorne up here.”
From behind her, Major Lorne answered, “I’m here, ma’am.”
Whirling around, she said, “Have you started a search for the colonel?”
“Yes, ma’am; I have teams sweeping Atlantis.”
“Have we done a sensor search for him?” Weir asked, glancing back at Chuck, who nodded.
“Yes, but nothing; can’t raise his COM, either.”
“Well, he didn’t just vanish and with this alarm going off, it’s out of character for him not to be here to see what’s going on. Find him, major.”
Lorne nodded, turned, and hurried down the gate room steps, passing a disheveled Dr. Rodney McKay on the way. McKay was engrossed in his pad display as he walked into the control room. Weir waited for a few moments, absently tapping her foot, until McKay decided to speak.
“I don’t know why the alarm went off.”
Weir leaned against a console, “You don’t know why?” McKay shrugged and Weir continued, “Does anyone know anything around here?” McKay started to answer but she kept talking, “A very loud and quite annoying alarm, which we have never heard before and didn’t know existed, goes off. and you have no idea why?”
“Elizabeth, we’ve been on Atlantis for over three years, but there’s a lot we don’t know about this place. So far, we are seeing some energy spikes in a section of the city that was flooded. It could be that some equipment has been activated and is shorting out; Zelenka has taken a team to investigate.”
“Then why aren’t you with them, Doctor?”
“Uh…you want me to go…with…” McKay nodded, “Going there now…” He started to leave but turned back, “No word about Sheppard?” Weir shook her head, and with a worried look on his face, McKay left, grabbing a Marine to accompany him.
~ooOoo~
Teyla and Ronon caught up with Major Lorne, as he was about to enter Sheppard’s quarters.
Ronon grunted, “Checked out his favorite path, nothing.”
Lorne punched in the override code and opened Sheppard’s door, “Nothing yet from any of the search teams, either.” They entered to find Sheppard’s quarters in its normal pristine shape.
Teyla remarked, “The bed has not been slept in, and it is nearly 0400 now. Major, have you noticed anything out of sorts with the colonel lately?”
“Other than taking a nap in his office this afternoon, or that he looks exhausted? Yeah, I was beginning to worry.”
“As were we, Major. I spoke to Doctor Beckett this evening regarding my concerns.” Her eyes widened as she realized perhaps Sheppard could be in the infirmary; she asked, “You have checked the infirmary.”
“This is Colonel Sheppard we’re talking about; the infirmary was the first place I looked.”
Ronon peered into the bathroom, “He’s not here; we’re wasting time.”
The trio stepped into the hallway as the voice of one of the search team leaders erupted from their COMs. “Major, we found Colonel Sheppard’s COM on the deck next to EP canal two.”
At a dead run, Lorne tapped his COM, “On our way.”
By the time, Lorne, Ronon, and Teyla arrived, the Marines had set up spotlights, and divers were about to enter the water. Ronon nearly jumped the railing before Lorne stopped him.
“No, let the rescue divers go in.”
Ronon was about to argue when one of the Marines holding a handheld searchlight yelled, “I’ve got him; he’s in one of the rafts.”
The divers immediately vaulted over the side, as the others hung over the railing, holding their collective breath until the first diver reached the raft Sheppard was lying in. A thumbs-up from the diver elicited an audible sigh of relief from everyone; Sheppard was alive. Lorne ordered a litter and called for Beckett and a medical team.
Working quickly, the Marine SAR unit raised Sheppard from the raft, a diver riding along to keep the litter from striking the hull. Beckett and his team rushed toward the colonel as the diver unhooked from the harness.
“Doctor, he’s unconscious, felt a huge lump on the right side of his skull. I think he might have hit his head on the motor.”
“Thanks, lad.” Beckett turned to the EMTs, “Lift this litter onto the gurney and let’s get him to the infirmary.”
Twenty minutes later, Elizabeth Weir and Rodney McKay rushed into the infirmary from opposite directions, nearly colliding. They found Ronon and Teyla waiting for Beckett to finish his preliminary exam on Sheppard. At Weir’s silent question, Teyla answered, “We do not know anything at the moment, only that he is unconscious.”
Turning to McKay, Weir asked, “Why didn’t we find him with the sensors?”
“We’ve experienced scanning issues with that area. There’s a major power conduit running along the water’s edge at that particular canal, seems to block the scans. Sheppard told me that the SOs use that particular canal because it has ladder access to the waterline. Leave it to Sheppard to be in the one area where we couldn’t find him.”
“Did you find anything on the West Pier?”
“Nothing so far but there is something going on. We traced a power surge to a corridor on the seventh floor in the circular tower. But we can’t access any of the rooms on the level; I sent Lorne to see if he can open it but his gene isn’t as strong as Sheppard or Beckett’s, so I doubt he can.”
“You can’t bypass it?”
“No, there are no door controls, believe me if there were, we’d be in there by now if …” McKay stopped as Beckett approached them, his expression worried.
“The good news is Colonel Sheppard’s vitals signs are stable, somewhat weak but stable. The not so good news is he has a mild concussion with some slight swelling from the blow he took above his right ear, and along with some minor bleeding in the ear canal.” Beckett paused, pursing his lips.
Quietly, Weir asked, “What else?”
“I…I don’t know; the Ancient scanner revealed his brain activity is very elevated.”
McKay asked, “Elevated, how?”
“The activity level is considerably stronger than in a healthy individual, much less someone with a head injury. Let me show you.” Beckett walked over to a terminal and brought up a digital scan, “It’s a mess; this is today’s scan, compared to the colonel’s baseline scan taken shortly after we arrived. You can see similarities here, and here,” as he pointed, “but these other lines, I don’t know why they are present.”
Teyla asked, “Is he in any danger?”
Beckett shrugged, “I simply don’t know how to answer that; once he regains consciousness we’ll know more. Elizabeth, Teyla came to me after dinner to tell me that John has been acting very strangely the last couple of weeks. He complained of headaches, seemed to become increasingly tired as the days passed. Have you noticed anything?”
“Yes, I spoke to him this morning after the briefing. He looked exhausted, distracted; I was worried. Of course, he told me he was fine, but I didn’t believe him.”
“Fine…” Beckett murmured, “No... he is far from fine.”
~ooOoo~
The familiar silhouette of Atlantis’ gate room materialized, as awareness crept into Sheppard’s consciousness. He felt disoriented, not certain how he ended up in the gate room; he was just on the South pier. Slowly, he pivoted in the darkened chamber to discover the stargate glowing, pale aqua light casting faint shadows on the walls.
As he climbed the steps toward the control room, the embedded lights engaged. Glancing around Sheppard realized he was alone and his heart thumped wildly in his chest. Where was everyone? As he pushed back against the adrenaline coursing through his body, he realized he wasn’t alone, he sensed a presence. An elusive presence he couldn’t identify.
Reaching the top landing, he walked to the stained-glass windows, revealing the city’s shimmering outline. Atlantis was underwater, as it was when they arrived. He stood mesmerized by the view, confusion replacing anxiety. He felt much like he did as he passed through the gate that day, a sense that somehow he was responsible for the city coming alive.
Whispering, he chastised himself, “The gene only activates equipment; it doesn’t control the city…”
“…Trust….”
A wispy voice echoed in the quiet; startled Sheppard turned toward the gate. “Who’s there?”
“You know…”
“No, I don’t…” he stopped. He did know; he had known since the first thought entered his consciousness, “Atlantis.”
As he uttered the city’s name, awareness surged into his mind, bringing white-hot pain; the image of the gate faded into darkness.
~ooOoo~
The infirmary was dark, only the dim light above Sheppard’s bed and the soft glow from the monitors revealed his team. Teyla sat quietly; her head bowed, meditating. Ronon slouched in a chair next to Sheppard’s bed. Rodney McKay was asleep, slumped against the wall, laptop precariously lying on his lap. The EEG’s shrill alarm startled Sheppard’s teammates and brought the night nurse to his bedside at a dead run.
McKay jumped straight up, Ronon grabbing his laptop before it hit the floor. “What….”
Ronon pulled him away from the bed, “Don’t know.”
Seconds later, Beckett rushed into the private room, quietly conferring with the nurse. After reviewing Sheppard’s vitals, he ordered, “Leigh, give him 50g of Osmitrol IV, and let’s get him to the Ancient scanner. I want another look at what’s going on. ”
Beckett turned toward Sheppard’s worried friends. “He’s had a spike in his already elevated brain activity. I’ve ordered meds to help relieve the increasing cranial pressure. The pressure is not life-threatening at the moment, but we need to determine what’s happening.”
Leigh returned bringing a syringe, which she injected into Sheppard’s ID port. Two attendants followed to move Sheppard’s gurney to the scanner.
“I’ll let you know as soon as I know something.” Beckett patted McKay on the shoulder, and followed the gurney.
Teyla wearily sank into a chair, “Rodney, what is this about a power surge?”
“When the alarm sounded, the control room techs noticed a huge energy spike coming from a building on the West Pier. We traced the spike to a room in the round building and located a doorway, but we were unable to open it; there are no access controls. Zelenka notified me a half-hour ago that Lorne attempted to open the door but his gene isn’t strong enough, and Beckett won’t leave Sheppard to try.”
Ronon asked, “Is the power still strong there?”
McKay nodded, “Yes, seems stable for now but something’s going on, and I have a very bad feeling about what’s happening.”
Twenty minutes later, Weir and Lorne arrived. “Teyla, Dr. Beckett just summoned us, what’s going on. Is John alright?”
“The pressure in his brain is increasing; Dr. Beckett gave him medication and has taken him back to the Ancient Scanner. He has not returned with any news.”
Lorne approached McKay, “Doc... I couldn’t get that door opened, I could feel it try to move, but I couldn’t make it happen.”
“It’s gonna take Sheppard to open it, if even he can. Zelenka’s checking the database for any mention of an energy source in the area and how to open that door; best we can do at the moment.”
Weir sighed, “At least, until John regains consciousness.” McKay simply nodded his agreement. They waited in silence for a few minutes before Beckett joined them. Weir immediately noticed how worried he looked, “Doctor, what’s wrong?"
“The secondary pattern showing up in Sheppard’s scan is more pronounced now, and I managed to differentiate them. There is another consciousness inside his brain, and it’s growing stronger.”
~ooOoo~
He was drifting, weightless, pitch-blackness surrounding him; visions of the gate room and of a submerged Atlantis flitted across his consciousness. His head was muddled, but he remembered; Atlantis spoke to him, her voice soft, melodic, soothing. As he thought of her, a pale aqua glow appeared in the dark. He shuddered as he realized the sensation he was feeling was her presence slipping into him.
“You’re with me again.”
Her voice was faint but becoming stronger, “I have always been present; you were not prepared to communicate with me. It has taken time to stimulate the area of your brain that can interact with my processor.”
“You caused the pain in my head…
“It was necessary; you are not as evolved as those who created me. The required electrical pathways in your brain had to be activated to allow you to communicate with me.”
“Why did you need to communicate with me?”
“My creator designed the city ships to choose a human possessing the strongest gene to interact with the artificial intelligence units. The system is quite complicated, and he wanted nothing left to chance. It is how the city ships survived for eons, there were no secrets between the city and those who live within.”
“I don’t understand.”
“In time, you will understand. You are injured, and my intrusion into your consciousness is harming you. I accelerated the process to strengthen your abilities when I realized that the Wraith remained a threat. The others who abandoned the city were stronger, and they could not defeat the Wraith; you would have no chance otherwise. Another danger exists, as well, a danger to my survival. I am withdrawing while you heal, but I will return. I cannot stop what is happening without your assistance, and we have little time.”
~ooOoo~
“Get me a cup.”
Dr. Radek Zelenka glanced over his shoulder toward the conference table, glaring at his department head. Rodney McKay was peering at his laptop screen, waving his empty coffee mug in the air. Zelenka sat down, letting his laptop thud as he placed it on the tabletop. “I am not your servant Rodney, get your own coffee.”
“Really, Zelenka…I’m trying to figure out what is wrong with Atlantis, and you can’t get me a cup of coffee.”
“Rodney, I have not slept for over twenty-four hours, while you have been cat-napping in the infirmary. Get your own coffee.”
Frowning, McKay rose, “I was in the infirmary because Sheppard is still unconscious.” He poured a cup of coffee and returned to his chair.
Zelenka slumped, exhaling a ragged breath, “I am sorry, Rodney; we are all tired.”
From the doorway, Elizabeth Weir agreed, “Yes…we are, Dr. Zelenka.” She entered the conference room, Major Lorne following. Without asking, the major poured coffee for Weir and himself, causing Rodney to glower at Zelenka.
Weir began, “Gentlemen, what do we know?”
Zelenka shrugged, “Very little at this point; the power seems to be building in the compartment we cannot access. We have yet to find anything in the database to explain what this area was used for or what the alarm signified.”
“Rodney, any ideas about what we are up against? Sheppard may have an alien consciousness residing in his brain. I’d really like to know if we are dealing with an intruder.”
“I’m loath to say it, but… no… no. I can tell you what I think it isn’t. What it is, I have no idea.”
“Doctor, I need to know, do I evacuate people to the Beta site or not?”
“Elizabeth, I don’t know. At the moment, it doesn’t appear whatever is going on in that room is building toward an explosion, but something is happening.”
Lorne leaned forward, “Doctor McKay that's not an answer.”
“That’s all I have, maj…”
Chuck’s urgent voice over their COMs silenced McKay. ”Dr. Weir, SGA-9 was scheduled to return from their mission at this time. The gate engaged then shut down; we no longer have power to the gate.”
McKay was already out the conference room door, Lorne hot on his heels. When they reached Chuck’s station and the DHD console, McKay shoved Chuck’s chair out of his way. Lorne grabbed the young lieutenant before he fell onto the deck.
McKay scanned the Ancient data display, pounding on several of the crystals, then turned to his laptop. After a couple of minutes, he looked at Chuck, “What did you do?”
“Nothing we don’t always do, Dr. McKay. SGA-9 was scheduled to dial in at 1100; they left at 0900 to take medical supplies to PS4-118, with plans to return in two hours. The gate engaged on time then went dark.”
“Rodney,” Elizabeth asked quietly, “what’s happened?”
“The only system that is affected is the power conduit to the stargate.”
“Why did it shut down?”
Zelenka cleared his throat, looking up from his laptop, “I can answer that, a power surge entered the gate’s power source seconds after the gate engaged. It originated in the building on the West Pier.”
“How many teams are out?”
Lorne replied, “Two; SGA-3 is at the Beta-site. Dr. Weir, both teams should be safe for the short run.”
“Well, there’s that.” Weir turned to McKay, “Rodney, figure this out, before it gets worse.”
~ooOoo~
Beckett sat next to Sheppard’s bed, pouring over the colonel’s latest tests. He insisted that Teyla and Ronon take a break, finally convincing them that he would remain with Sheppard while they had a hot meal.
Closing his eyes, he went over the test results in his head. Sheppard was improved; the cranial pressure had dropped, and the scanner showed only one electrical pattern on the EEG. What puzzled him was the fact Sheppard was exhibiting neural impulses in a section of his brain where humans were normally dormant.
“Carson, you awake?”
“Ah, Elizabeth, come sit down.”
“Where are Teyla and Ronon?”
“I convinced them to have dinner and rest for a while.” He chuckled, “Which means they left about fifteen minutes ago…they’ll be back shortly.”
Elizabeth laughed softly, as she brushed her hair behind her ear, “Yes they will. How is he?”
“Resting better, pressures down and there is much less activity going on in there.”
“I hear some hesitation in your voice, what are you not telling me?”
He turned his view screen for her to see, “The second pattern is gone, but these wiggles right here represent activity in an area …uh… humans don't have activity.”
Sucking in a deep breath, she replied, “Are you saying that whatever entered John’s brain has altered it?”
“Yes, I am…whether it’s a permanent change or simply residual current from the other pattern, it’s too early to tell. I do think from the results of these latest tests he’s going to wake up soon.”
“At least, there is some good news, we’re not making much progress in determining what’s happening.” Weir was updating Beckett on the science team’s efforts when Ronon and Teyla returned, quickly recapping for them.
Teyla shivered, “You are telling us, Dr. Weir, that Rodney has made no progress.”
“Yes, in simple terms, we know nothing more than we did when the alarm sounded. I…”
Ronon stopped her, “He’s moving.”
Beckett jumped up and leaned over the colonel, “John, can you hear me?” He gently shook Sheppard’s shoulder, “John…wake up.” Sheppard's eyes fluttered open slightly; he tried to speak but his voice was weak.
“It’s okay, laddie, just rest. It’s good enough that you are awake, even for a few minutes.”
Turning to call for the nurse, Beckett stopped when Sheppard grasped his arm. His voice feeble, the colonel murmured, “A-At…lantis…dan…ger.”
Sheppard had fallen back into a deep sleep by the time McKay arrived in the infirmary. As he blustered into the private room, Teyla shushed him.
“Rodney, please be quiet, John is asleep.”
“What did he say…Atlantis is in danger? Wake him up.”
Weir answered, “Yes, he said Atlantis is in danger, and no... we are not waking him.”
“What kind of danger? What else did he say?”
‘Nothing else, Rodney; he’s very weak, but Carson thinks he will begin to wake up for longer periods. We’ll find out what he meant then.”
“We need to know…I just got word that the power levels are increasing in that room, and we are beginning to lose power in some areas of the city.”
Weir stood up, “When did this start?”
“As of fifteen minutes ago, the power drainage remained slight, predominantly in areas that we don’t access often. Elizabeth, we need Sheppard to figure out what’s going on.”
~ooOoo~
Sheppard noticed the aroma of coffee first, then the smell of antiseptic and the flowery detergent the laundry used to wash the sheets. Surprisingly, he felt comfort rather than distress; he was in the infirmary, and this had to be real.
He struggled to open his eyes, managing only narrow slits to start with. The coffee aroma along with the sound of faint tapping could only mean one thing; McKay was nearby.
“McK-ay…coffee….”
A yelp of surprise and the sound of something striking the floor was quickly followed by McKay’s voice “Sheppard... you’re awake.”
“Yeah…coffee…h-head hurts…”
“I’ll be back, going to get Beckett.”
McKay rushed from the room, and Sheppard heard him contact Elizabeth before his voice faded away. His vision was clearing and he gazed around, realizing he was in one of the trauma rooms.
“Crap,” he whispered, “must be bad.” Woozy, he lost track of time until he heard Beckett’s soothing brogue.
“John, you still awake?”
Sheppard slowly opened his eyes, “Uh huh…head…hurts.”
“No doubt, laddie; you fell into one of the rafts in the canal, hit your head on a motor. But you’re gonna be fine, just need to rest.” Beckett whispered quietly to the nurse, then continued, “I’m going to give you something for the pain, and let you sleep.”
“C-coffee…”
“I promise you can have a cuppa when you wake up, now you need to sleep.” Beckett turned to watch as the nurse injected pain medication into the IV port, when Sheppard grabbed his arm.
“No…n-need to wake...up…At-lantis…in trouble…”
“How do you know?”
“T-told me,” Sheppard’s voice trailed off as he drifted to sleep.
Six hours later, as Weir approached the conference room, the sound of McKay and Zelenka’s bickering drifted through the doors. She sucked in a deep breath and entered.
“So, I’m assuming you two haven’t figured out what’s going on.”
McKay looked up quickly, “What makes you think that?”
“Do you?”
“Uh…no, we don’t. Zelenka hasn’t been able to decipher any of the data we’re receiving.”
Glowering at McKay, Zelenka spoke, “What we do know, Dr. Weir, is that the power drain continues, but at a slow pace.”
“Where have we lost power, besides to the gate?”
“Currently, power loss is confined to the uninhabited sections of the city, but the outages beginning to affect some of the Ancient equipment. We have shut down as much equipment as we can and still maintain citywide sensors.”
McKay added, “The energy signal coming from that room has remained steady for the last several hours. There is no question that the outages are a result of the energy surges coming from that room.”
“Doctors, we need answers.”
“What we need is Sheppard; did he wake up again?”
Weir shook her head, “Not yet, but Carson says his brain scans are more stable. At the moment, he’s sleeping and Carson refuses to wake him up.” She pursed her lips, “Do you have any idea what John meant when he said someone told him that Atlantis was in danger?”
“Not a clue…unless whatever alien was inside his head told him.”
“Rodney, do you really think there was an alien entity in John’s head?”
“After what we’ve seen these last two years, I’d believe just about anything.”
“But from where, how…” Weir stopped, listening to her COM. She stood up, “That was Beckett, John’s waking up. Maybe we can now find out what he meant.” Weir and McKay headed for the infirmary.
~ooOoo~
The thick fog swirling in his head was slowly lifting. Opening his eyes, Sheppard first thought there were dark shadows on the walls, but as his vision cleared, he realized it was Ronon and Beckett.
“Hey…”
Ronon spun around, “Sheppard...
“Yeah…t-think it’s…me.” He struggled to sit up, but Ronon held him down. “Oh…okay, I’ll just stay h-here.”
“Aye, laddie, exactly what you should do.” Beckett appeared at Sheppard’s bedside, “Now, how do you feel?”
Sheppard scoffed, “Not great…but I need to get out of here.”
“You are doing no such thing; you have had a serious injury and….”
“N-No… gotta get up.” Sheppard again attempted to sit up, but Ronon’s hand on his shoulder stopped him. Sighing deeply, and his voice weak, “You don’t understand, I have to get up.”
Weir and McKay arrived, and Weir asked, “Why do you need to get up?”
“A-Atlantis…in trouble…”
“How do you know that there’s a problem on Atlantis? Did you hear the alarm?”
“Alarm…I…think maybe…sharp pain in my head…woke up…h-here.” Sheppard tried to sit up again, and this time Beckett helped him by raising the head of the bed.
Weir asked, “John, Dr. Beckett said someone told you Atlantis is in danger.”
Sheppard dropped his head, reluctant to answer her fully, “Someone…did.”
Beckett interjected, “You’ve been having headaches for several days, haven’t you?” Sheppard nodded and Beckett continued, “Your initial brain scans showed enormous activity, there were two separate patterns at one time, and now…”
“Now?”
“Now, whatever was inside you has vanished, but…it left you with areas of your brain more developed than before.”
Sheppard gave Beckett a faint half-smile, “She…said she had to rewire me…to help her.”
Weir asked, “Who had to ‘rewire’ you?”
Quietly, he answered, “Atlantis.”
McKay blurted, “Atlantis? What do you mean Atlantis told you?”
Sheppard rubbed his forehead, “She can…talk to me…” he grimaced dropping his head.
Beckett lowered the bed, “Alright, everyone out. I’m giving him something for the pain, and then he needs to rest.”
Weir, McKay, along with Teyla and Ronon stepped into the main infirmary ward, all noticeably shaken. Teyla spoke first, “Could John really be talking to Atlantis?”
Weir shrugged, “We know he can control Ancient equipment better than anyone, I…” she stopped, turning to McKay, “Is it possible that the gene would allow Atlantis’ computer core to communicate with him?”
“The brain generates electricity; the computer core is powered by electricity generated by the Zed PM. I suppose it’s possible; the gene may provide receptors to accept signals from the core.” He paused, then added, a note of skepticism in his voice, “It could be conceivable...maybe."
Teyla asked, “He said ‘she’; was he referring to Atlantis the same way as you refer to the jumpers, as female?
McKay sighed, “Could be, but knowing Sheppard’s luck with Ancient women Atlantis probably is a girl.”
Weir returned to her office a few hours later, after an unsuccessful attempt at getting some sleep. Grabbing a cup of coffee, she reviewed the reports coming in from Lorne. The major was overseeing the scientists who were attempting to enter the mysterious room. Beckett agreed to try to open the door once he was satisfied that Sheppard was resting comfortably, but Lorne reported Beckett failed as well.
Leaning back in her chair, Weir closed her eyes, resting her hands on her forehead. She nearly fell from her chair when the self-destruct alarm shattered the quiet. Jumping to her feet, she dashed into the control room, where Lian, the night gate tech was typing furiously on his keyboard.
“What’s caused the self-destruct to engage?”
Lian shook his head, “I don’t know, Dr. Weir. I’ve started running a diagnostic, but nothing appears to be out of the ordinary.”
She tapped her COM, “McKay, get to the control room now.”
~ooOoo~
“Colonel Sheppard, can you hear me?”
Sheppard struggled to comprehend, “Atlantis?”
“I need your assistance; the ark is awakening.”
“The ark…what’s…the ark?”
“I will explain, but you must be conscious to assist me. I need to finish creating the neural pathway for you to fully interact with me. It will take both of us to stop the ark.”
“What do I need to do?”
“Allow me to guide to you, open your mind.”
Sheppard felt a warmth flood through his body and began to wake.
Carson Beckett was asleep on a cot, stashed in his small office, only a few steps from Sheppard’s private room. Once the colonel was sleeping soundly, Beckett finally convinced Ronon and Teyla to rest in their quarters. They agreed but only after he assured them he would stay in the infirmary. After they departed, Beckett told the night nurse, he never promised them he wasn’t going to sleep as well.
He was snoring lightly when the self-destruct alarm sounded. Waking abruptly, he was getting up as Leigh opened the door, “Dr. Beckett, its Colonel Sheppard. I just checked on him; he's not in the infirmary.”
Beckett brushed past the nurse as he tapped on his COM, his voice gruff, “Lorne, Beckett here…Colonel Sheppard has left the infirmary without authorization. I need you to find him.”
~ooOoo~
Thankful that he knew the city’s layout better than anyone, Sheppard took back corridors to reach his quarters. The door opened silently and Sheppard slipped inside, confident he had not been seen. Stripping off the infirmary scrubs, he grabbed a pair of track pants, a t-shirt, and a hoodie and dressed. As he sat down to put on his running shoes, he felt a now recognizable sensation enter his consciousness…Atlantis.
“You’re here.”
“Very good, you can now sense as I join with you.”
“Join…? Oh...okay…” Sheppard shuddered slightly, as a wave of pain passed through his head. “Uh, you need to tell me what’s…happening, the self-destruct just sounded. What…kind of danger are we in?”
“In less than four hours, I will be destroyed.”
Sheppard felt the flush of adrenaline spread through his body, but his voice, although weak, remained calm, “Then we need to get started, but first I need to get out of here. They’ll be looking for me.”
Atlantis directed him through little-used corridors, twice preventing him from being intercepted by Marines searching for him. She led him to an area the expedition had yet to explore, a small chamber in on the North pier, three decks below the water line. The chamber contained an Ancient console, a conference table, and several familiar white couches. The console and the light towers began to glow as Sheppard entered.
“Where are we?” Sheppard asked as he sat down on the nearest couch, exhausted from the trek.
“This is an auxiliary control center for the sensors located on the hull. During space flight, if the control tower was otherwise engaged, technicians would use this console to monitor the sensors for anomalies.”
“Otherwise engaged? Do you mean on a scientific mission or in combat?”
“You suspect my history extends far beyond the difficulties with the Wraith, and you would be correct. I was built for scientific exploration and as a means to spread humanity across the vastness of space. Along the way, there were many encounters, and I will provide all of that information to you in due time. I need for you to allow me access to your mind; if you do not resist it will not be as painful. I have nearly completed the neural pathway allowing us to communicate freely.”
Sheppard swallowed deeply; his head hurt badly enough, but he had to risk allowing Atlantis to finish her task. “What do I need to do?”
“I suggest you lie down and relax; this will not take long.”
Grimacing as Atlantis deepened their connection, he was relieved the pain was less intense as she had promised. The normal background hum of the city he sensed from the moment he first emerged through the gate was becoming stronger. Sheppard felt connected to Atlantis from the beginning and when he traveled off world or to the mainland, he felt uneasy, as if part of him had been left behind. When the Ancients returned only a few months before and reclaimed the city, he felt lost during the month on Earth and joyous when they retook Atlantis from the Replicators. Aware he should have been dismayed the Replicators murdered the Ancients, knowing what secrets the builders of the city possessed, he had instead been elated they could return to the place he felt at home.
As his thoughts drifted to the days after returning to Atlantis, Sheppard lost track of time. He was startled when he heard the soft voice in his head calling his name.
“John, can you hear me?”
“Yes, sorry…I was thinking about something…” A wave of panic crept into his throat, “Can…can you tell what...I’m thinking?”
“No, I am unable to read your thoughts, only to communicate when you accept my entry. I can perceive your emotions. My creator believed that the artificial intelligence processors should be capable of more than operating the cityships. He rewrote the code to include the ability for the processors to interact with someone who possessed an extremely strong gene.”
Sheppard exhaled deeply, reassured Atlantis wasn’t telepathic. He noticed her voice was stronger, richer, as though she was standing beside him. “Are you done?”
“I have completed the procedure of stimulating the dormant neural paths within your brain. It will take time for you to understand how to utilize your new capabilities. At this time, it is imperative that I be able to communicate with you. I cannot stop what is occurring, but I can convey what needs to be done to you.”
“What do you need for me to do?”
“I believe the place to start is for you to understand why we can communicate. My creator left a file as an explanation for my muses. Please relax and open your mind.”
Sheppard closed his eyes. In the darkness, a faint light appeared, then morphed into an image of a tall, lean man sitting before a bank of consoles, much like those on Atlantis. His dark hair, patrician features, and serious gray eyes gave the man an aura of distinction. When he spoke, his voice was deep, commanding.
“I am Adalricus Ludo, a member of the Alteran Science Praeclarum. I realize you have many questions, most of which can be answered by Atlantis. I will only give you a brief overview of the cityships and the Artificial Intelligence Processor residing on the ships, in particular, the AIP on this ship.
Artificial Intelligence Processor1187719-07, holds the designation Atlantis. She is one of seven cityships built to soar among the stars, bringing life to barren worlds, and knowledge to existing worlds. Atlantis was built on Altera Seven, one of seven worlds the original Alterans colonized as they spread across space. A cityship was built on each world to carry the Altarens’ message.”
Ludo stood up and walked toward a monitor displaying a schematic of a cityship. “The AI processors were designed to be the operating systems of the cityships. I realized that it was one thing to be able to sense the need to open a door, raise a shield, or engage the stardrive. I also realized that the cityships would most likely never return to their home worlds. I believed that the AIs needed the ability to learn, to grow, to understand humans, their emotions, their fears, their joys. I wanted them to interact on a level that the Alterans had never been able to accomplish before.”
Hesitating for a moment, he gazed at the monitor, then continued, “I knew many of my colleagues, and the Alteran Council would vehemently disapprove of my plan; they valued logic and science over emotion. Covertly, I rewrote the code giving the AIs the ability to respond to the person who possessed the strongest ability to interact with the technology. All Alterans could sense the technology due to the gene they possessed, the gene that responds to the frequencies created by the crystal-based systems. However, only a minority of Alterans possessed a gene strong enough to interact with the code I embedded. That person, muse, would be able to hear and converse with the AI, who, in turn, would learn from their muse.”
Ludo paused again, “I will most likely never know the outcome of my actions. I only hope muse and AI grow and learn together. If you are viewing this message, then you possess the gene capable of interacting with the AI. Please use your ability wisely and remember the purpose of the cityship, to gain and spread knowledge.”
Ludo’s image faded from his consciousness, and Sheppard opened his eyes. In the dim light, his eyes fell to the console in the middle of the room. Ludo could have been standing in that spot when he recorded his message. He was overwhelmed with the realization, of how much they didn’t know about the Alterans. There was a great deal he wanted to ask Atlantis but now was not the time. He sat up slowly, dizzy, his head pounding.
“Atlantis, what’s the danger from?”
“Several thousand years ago, I was directed to a region called the Galleré. The Galleré formed a passageway between two massive nebulas in an area rich with young solar systems. The leaders of the city spent many generations there, over two thousand years, seeding suitable planets, exploring the nebulas. Much was learned during that time, but one day, a shuttle returned from a mission with news of a planet where humanoid life had developed independently. There was much excitement, and against the wishes of many of the governing council, the Administrator ordered a return mission, this time not cloaking the shuttle but initiating contact.”
“I take the contact didn’t go well.”
“You are correct; it did not. There was no confrontation but the contact lead to dissidence. The humanoids called themselves the Iriki. They lived alone with only the nebulas in the sky for companionship, peaceful people, with no technology, an agrarian society. They were curious about the city, not frightened at all. In their usual manner, the Altarens offered their expertise to improve their crops, their dwellings, introducing them to technology. The Iriki resisted. They decided that our technology was not for them and asked the Altarens to leave.”
“Did the Altarens refuse?”
“No, they adhered to the Irikis wishes and did not contact them again, although that was not the last heard of the Iriki philosophy. As the weeks and months passed, it became clear that a group of Altarens, who knew no other existence than living on Atlantis had been influenced by the simplicity of the Iriki lifestyle. They chose to turn away from technology and begged the Administrator to return them to Iriki, so they could live out their lives on the planet. The Administrator refused, which made the dispirited Alterans even more dispirited. I was directed to depart from the area a few months later, contact with the Iriki all but forgotten.”
Sheppard dropped his head onto the back cushion, closing his eyes, “Forgotten by everyone but the ones who wanted to stay behind.”
“Yes, you are correct; they were determined to change the Alteran philosophy, regardless of the amount of time it would take. The dissidents were very careful, their actions unknown. The members of The Order of Libét as it was later learned they called themselves, remained secretive, hiding their members and numbers from the others. The Order of the Libét remained undetected until thousands of years later when the Alterans, faced with defeat by the Wraith, decided to abandon the city.”
“How did they find out?”
“Members of the Libét volunteered to be part of the advance scout team, returning to Earth to assess the conditions and determine where the population would settle. They followed through with their responsibilities and located suitable areas for habitation. Departure schedules were created, but one night prior to the exodus two hundred and seventy-three people gated off the city covertly never to be heard from again.”
“That’s a lot of people, no one noticed?”
“As now, there were few technicians on duty during the night hours, and they disappeared also. With so much to do, the city leaders chose to ignore their departure and turned to other tasks. There was much activity; the scientists were busy copying data from my storage banks to take with them. Their hope was to return someday and wanted the data preserved.”
“Atlantis, why are you taking time to tell me this…don’t we need to stop this ark thing?”
“Yes, and we now have three hours to do so, but it is important that you know what occurred. Only a short time before your Administrator arrived…”
“Elizabeth?”
“Yes, just before she arrived, a scientist discovered an encrypted file embedded in my central core and notified the man you know as Janus. He became intrigued and worked feverishly to open the data. He accomplished his task, and discovered what the Libét had done.”
Sheppard was surprised that Atlantis seemed to pause for dramatic effect; she definitely adapted human behavior. “What had they done?”
“Do not forget the members of the order were Alterans, and they continued to live here. Many members became scientists to acquire the skills to accomplish their goal. They may have abhorred technology, but they employed it in a plot to destroy the city. Plans they had formulated many, many years prior, waiting for the opportunity to destroy the cityship, were initiated when the decision was made to abandon the city. Plans to be activated should the Alterans return.”
“I’m assuming that the alarm that sounded was because of the Libét, but why?”
“When I began to assist you in developing your ability to use the gene, they discovered you. As you grew stronger, the sensors put in place began to notice you; when you were identified as a muse, the Ark was activated. I sounded the alarm in an attempt to warn you of the danger.”
“This ark, is it a bomb?”
“It is an incendiary device and you are the detonator.”
Author: stella_pegasi
Recipient: ArtisticAbandon
Word Count: ~16,800
Rating: PG
Warnings: Minor language, whump
Summary: There is an intruder on Atlantis, who may cost John Sheppard his life.
Author Notes: Many thanks to black_raven135 for being the beta for this story. As always, I appreciate her keen eye and insight.
By stella_pegasi
Part One
John Sheppard moved silently along the darkened passageway, trying to concentrate on the soothing resonance of the waves lapping at Atlantis’ hull. Night after night, he roamed unexplored sections of the city, trying to escape the sounds in his head.
Without thinking, he changed direction abruptly and exited the passageway onto the deck; the doors opening without a conscious thought. He sucked in salty fresh air, rubbing his temples as he exhaled. Nothing helped; the sounds remained. In the bright moonlight, he walked to the railing surrounding the open section of the hull nicknamed the canal, and peered over the side, gazing at the inflatable rafts special ops used to train divers. The small rafts bobbed up and down with the gentle waves.
Leaning his elbows on the railing, he cradled his pounding head, making a vain attempt to will away the pain. But the sensation wouldn’t go away; the nagging feeling that someone was calling his name, that someone was with him. An impression of urgency, yet when he tried to concentrate, he couldn’t quite grasp the thought.
Sheppard was exhausted, sleep elusive, hindered by the pain. People were beginning to notice; Weir asked him at the morning briefing if he was all right, while Lorne caught him napping in the middle of the afternoon. At dinner, Teyla’s telltale eyebrow arched when he told her he was fine; she clearly didn’t believe him. After dinner, when he heard Beckett was looking for him, he knew she’d tattled. He never cared for busybodies; he was just fine.
He scoffed, “Yeah, John, keep telling yourself that; you’re just fine.”
He blew out a deep breath, knowing he wasn’t fine and debating with himself about going to Beckett. He hadn’t quite convinced himself when a claxon blared, the loud, grating sound startling him as intense pain flooded his head. Grabbing his head, he lost his footing and slipped over the railing, landing in one of the inflatable rafts, unconscious.
~ooOoo~
Dr. Elizabeth Weir stood, arms crossed, glaring at Senior Gate Technician Lt. Chuck Campbell. “What do you mean you can’t find him? How can you possibly not know where Colonel Sheppard is?”
“Ma’am, he’s not in his quarters, and his team hasn’t seen him since dinner. Teyla and Ronon are tracing his normal running route to see if he decided to go for a run.”
She sighed, “He couldn’t…” the claxon blared again, interrupting her. Through gritted teeth, she said, “Can you turn that thing off?”
Chuck quickly pressed a series of crystals on the control panel, “Sorry, Dr. Weir, I thought I had turned it off.”
“As I was saying, Sheppard didn’t just vanish, get Lorne up here.”
From behind her, Major Lorne answered, “I’m here, ma’am.”
Whirling around, she said, “Have you started a search for the colonel?”
“Yes, ma’am; I have teams sweeping Atlantis.”
“Have we done a sensor search for him?” Weir asked, glancing back at Chuck, who nodded.
“Yes, but nothing; can’t raise his COM, either.”
“Well, he didn’t just vanish and with this alarm going off, it’s out of character for him not to be here to see what’s going on. Find him, major.”
Lorne nodded, turned, and hurried down the gate room steps, passing a disheveled Dr. Rodney McKay on the way. McKay was engrossed in his pad display as he walked into the control room. Weir waited for a few moments, absently tapping her foot, until McKay decided to speak.
“I don’t know why the alarm went off.”
Weir leaned against a console, “You don’t know why?” McKay shrugged and Weir continued, “Does anyone know anything around here?” McKay started to answer but she kept talking, “A very loud and quite annoying alarm, which we have never heard before and didn’t know existed, goes off. and you have no idea why?”
“Elizabeth, we’ve been on Atlantis for over three years, but there’s a lot we don’t know about this place. So far, we are seeing some energy spikes in a section of the city that was flooded. It could be that some equipment has been activated and is shorting out; Zelenka has taken a team to investigate.”
“Then why aren’t you with them, Doctor?”
“Uh…you want me to go…with…” McKay nodded, “Going there now…” He started to leave but turned back, “No word about Sheppard?” Weir shook her head, and with a worried look on his face, McKay left, grabbing a Marine to accompany him.
~ooOoo~
Teyla and Ronon caught up with Major Lorne, as he was about to enter Sheppard’s quarters.
Ronon grunted, “Checked out his favorite path, nothing.”
Lorne punched in the override code and opened Sheppard’s door, “Nothing yet from any of the search teams, either.” They entered to find Sheppard’s quarters in its normal pristine shape.
Teyla remarked, “The bed has not been slept in, and it is nearly 0400 now. Major, have you noticed anything out of sorts with the colonel lately?”
“Other than taking a nap in his office this afternoon, or that he looks exhausted? Yeah, I was beginning to worry.”
“As were we, Major. I spoke to Doctor Beckett this evening regarding my concerns.” Her eyes widened as she realized perhaps Sheppard could be in the infirmary; she asked, “You have checked the infirmary.”
“This is Colonel Sheppard we’re talking about; the infirmary was the first place I looked.”
Ronon peered into the bathroom, “He’s not here; we’re wasting time.”
The trio stepped into the hallway as the voice of one of the search team leaders erupted from their COMs. “Major, we found Colonel Sheppard’s COM on the deck next to EP canal two.”
At a dead run, Lorne tapped his COM, “On our way.”
By the time, Lorne, Ronon, and Teyla arrived, the Marines had set up spotlights, and divers were about to enter the water. Ronon nearly jumped the railing before Lorne stopped him.
“No, let the rescue divers go in.”
Ronon was about to argue when one of the Marines holding a handheld searchlight yelled, “I’ve got him; he’s in one of the rafts.”
The divers immediately vaulted over the side, as the others hung over the railing, holding their collective breath until the first diver reached the raft Sheppard was lying in. A thumbs-up from the diver elicited an audible sigh of relief from everyone; Sheppard was alive. Lorne ordered a litter and called for Beckett and a medical team.
Working quickly, the Marine SAR unit raised Sheppard from the raft, a diver riding along to keep the litter from striking the hull. Beckett and his team rushed toward the colonel as the diver unhooked from the harness.
“Doctor, he’s unconscious, felt a huge lump on the right side of his skull. I think he might have hit his head on the motor.”
“Thanks, lad.” Beckett turned to the EMTs, “Lift this litter onto the gurney and let’s get him to the infirmary.”
Twenty minutes later, Elizabeth Weir and Rodney McKay rushed into the infirmary from opposite directions, nearly colliding. They found Ronon and Teyla waiting for Beckett to finish his preliminary exam on Sheppard. At Weir’s silent question, Teyla answered, “We do not know anything at the moment, only that he is unconscious.”
Turning to McKay, Weir asked, “Why didn’t we find him with the sensors?”
“We’ve experienced scanning issues with that area. There’s a major power conduit running along the water’s edge at that particular canal, seems to block the scans. Sheppard told me that the SOs use that particular canal because it has ladder access to the waterline. Leave it to Sheppard to be in the one area where we couldn’t find him.”
“Did you find anything on the West Pier?”
“Nothing so far but there is something going on. We traced a power surge to a corridor on the seventh floor in the circular tower. But we can’t access any of the rooms on the level; I sent Lorne to see if he can open it but his gene isn’t as strong as Sheppard or Beckett’s, so I doubt he can.”
“You can’t bypass it?”
“No, there are no door controls, believe me if there were, we’d be in there by now if …” McKay stopped as Beckett approached them, his expression worried.
“The good news is Colonel Sheppard’s vitals signs are stable, somewhat weak but stable. The not so good news is he has a mild concussion with some slight swelling from the blow he took above his right ear, and along with some minor bleeding in the ear canal.” Beckett paused, pursing his lips.
Quietly, Weir asked, “What else?”
“I…I don’t know; the Ancient scanner revealed his brain activity is very elevated.”
McKay asked, “Elevated, how?”
“The activity level is considerably stronger than in a healthy individual, much less someone with a head injury. Let me show you.” Beckett walked over to a terminal and brought up a digital scan, “It’s a mess; this is today’s scan, compared to the colonel’s baseline scan taken shortly after we arrived. You can see similarities here, and here,” as he pointed, “but these other lines, I don’t know why they are present.”
Teyla asked, “Is he in any danger?”
Beckett shrugged, “I simply don’t know how to answer that; once he regains consciousness we’ll know more. Elizabeth, Teyla came to me after dinner to tell me that John has been acting very strangely the last couple of weeks. He complained of headaches, seemed to become increasingly tired as the days passed. Have you noticed anything?”
“Yes, I spoke to him this morning after the briefing. He looked exhausted, distracted; I was worried. Of course, he told me he was fine, but I didn’t believe him.”
“Fine…” Beckett murmured, “No... he is far from fine.”
~ooOoo~
The familiar silhouette of Atlantis’ gate room materialized, as awareness crept into Sheppard’s consciousness. He felt disoriented, not certain how he ended up in the gate room; he was just on the South pier. Slowly, he pivoted in the darkened chamber to discover the stargate glowing, pale aqua light casting faint shadows on the walls.
As he climbed the steps toward the control room, the embedded lights engaged. Glancing around Sheppard realized he was alone and his heart thumped wildly in his chest. Where was everyone? As he pushed back against the adrenaline coursing through his body, he realized he wasn’t alone, he sensed a presence. An elusive presence he couldn’t identify.
Reaching the top landing, he walked to the stained-glass windows, revealing the city’s shimmering outline. Atlantis was underwater, as it was when they arrived. He stood mesmerized by the view, confusion replacing anxiety. He felt much like he did as he passed through the gate that day, a sense that somehow he was responsible for the city coming alive.
Whispering, he chastised himself, “The gene only activates equipment; it doesn’t control the city…”
“…Trust….”
A wispy voice echoed in the quiet; startled Sheppard turned toward the gate. “Who’s there?”
“You know…”
“No, I don’t…” he stopped. He did know; he had known since the first thought entered his consciousness, “Atlantis.”
As he uttered the city’s name, awareness surged into his mind, bringing white-hot pain; the image of the gate faded into darkness.
~ooOoo~
The infirmary was dark, only the dim light above Sheppard’s bed and the soft glow from the monitors revealed his team. Teyla sat quietly; her head bowed, meditating. Ronon slouched in a chair next to Sheppard’s bed. Rodney McKay was asleep, slumped against the wall, laptop precariously lying on his lap. The EEG’s shrill alarm startled Sheppard’s teammates and brought the night nurse to his bedside at a dead run.
McKay jumped straight up, Ronon grabbing his laptop before it hit the floor. “What….”
Ronon pulled him away from the bed, “Don’t know.”
Seconds later, Beckett rushed into the private room, quietly conferring with the nurse. After reviewing Sheppard’s vitals, he ordered, “Leigh, give him 50g of Osmitrol IV, and let’s get him to the Ancient scanner. I want another look at what’s going on. ”
Beckett turned toward Sheppard’s worried friends. “He’s had a spike in his already elevated brain activity. I’ve ordered meds to help relieve the increasing cranial pressure. The pressure is not life-threatening at the moment, but we need to determine what’s happening.”
Leigh returned bringing a syringe, which she injected into Sheppard’s ID port. Two attendants followed to move Sheppard’s gurney to the scanner.
“I’ll let you know as soon as I know something.” Beckett patted McKay on the shoulder, and followed the gurney.
Teyla wearily sank into a chair, “Rodney, what is this about a power surge?”
“When the alarm sounded, the control room techs noticed a huge energy spike coming from a building on the West Pier. We traced the spike to a room in the round building and located a doorway, but we were unable to open it; there are no access controls. Zelenka notified me a half-hour ago that Lorne attempted to open the door but his gene isn’t strong enough, and Beckett won’t leave Sheppard to try.”
Ronon asked, “Is the power still strong there?”
McKay nodded, “Yes, seems stable for now but something’s going on, and I have a very bad feeling about what’s happening.”
Twenty minutes later, Weir and Lorne arrived. “Teyla, Dr. Beckett just summoned us, what’s going on. Is John alright?”
“The pressure in his brain is increasing; Dr. Beckett gave him medication and has taken him back to the Ancient Scanner. He has not returned with any news.”
Lorne approached McKay, “Doc... I couldn’t get that door opened, I could feel it try to move, but I couldn’t make it happen.”
“It’s gonna take Sheppard to open it, if even he can. Zelenka’s checking the database for any mention of an energy source in the area and how to open that door; best we can do at the moment.”
Weir sighed, “At least, until John regains consciousness.” McKay simply nodded his agreement. They waited in silence for a few minutes before Beckett joined them. Weir immediately noticed how worried he looked, “Doctor, what’s wrong?"
“The secondary pattern showing up in Sheppard’s scan is more pronounced now, and I managed to differentiate them. There is another consciousness inside his brain, and it’s growing stronger.”
~ooOoo~
He was drifting, weightless, pitch-blackness surrounding him; visions of the gate room and of a submerged Atlantis flitted across his consciousness. His head was muddled, but he remembered; Atlantis spoke to him, her voice soft, melodic, soothing. As he thought of her, a pale aqua glow appeared in the dark. He shuddered as he realized the sensation he was feeling was her presence slipping into him.
“You’re with me again.”
Her voice was faint but becoming stronger, “I have always been present; you were not prepared to communicate with me. It has taken time to stimulate the area of your brain that can interact with my processor.”
“You caused the pain in my head…
“It was necessary; you are not as evolved as those who created me. The required electrical pathways in your brain had to be activated to allow you to communicate with me.”
“Why did you need to communicate with me?”
“My creator designed the city ships to choose a human possessing the strongest gene to interact with the artificial intelligence units. The system is quite complicated, and he wanted nothing left to chance. It is how the city ships survived for eons, there were no secrets between the city and those who live within.”
“I don’t understand.”
“In time, you will understand. You are injured, and my intrusion into your consciousness is harming you. I accelerated the process to strengthen your abilities when I realized that the Wraith remained a threat. The others who abandoned the city were stronger, and they could not defeat the Wraith; you would have no chance otherwise. Another danger exists, as well, a danger to my survival. I am withdrawing while you heal, but I will return. I cannot stop what is happening without your assistance, and we have little time.”
~ooOoo~
“Get me a cup.”
Dr. Radek Zelenka glanced over his shoulder toward the conference table, glaring at his department head. Rodney McKay was peering at his laptop screen, waving his empty coffee mug in the air. Zelenka sat down, letting his laptop thud as he placed it on the tabletop. “I am not your servant Rodney, get your own coffee.”
“Really, Zelenka…I’m trying to figure out what is wrong with Atlantis, and you can’t get me a cup of coffee.”
“Rodney, I have not slept for over twenty-four hours, while you have been cat-napping in the infirmary. Get your own coffee.”
Frowning, McKay rose, “I was in the infirmary because Sheppard is still unconscious.” He poured a cup of coffee and returned to his chair.
Zelenka slumped, exhaling a ragged breath, “I am sorry, Rodney; we are all tired.”
From the doorway, Elizabeth Weir agreed, “Yes…we are, Dr. Zelenka.” She entered the conference room, Major Lorne following. Without asking, the major poured coffee for Weir and himself, causing Rodney to glower at Zelenka.
Weir began, “Gentlemen, what do we know?”
Zelenka shrugged, “Very little at this point; the power seems to be building in the compartment we cannot access. We have yet to find anything in the database to explain what this area was used for or what the alarm signified.”
“Rodney, any ideas about what we are up against? Sheppard may have an alien consciousness residing in his brain. I’d really like to know if we are dealing with an intruder.”
“I’m loath to say it, but… no… no. I can tell you what I think it isn’t. What it is, I have no idea.”
“Doctor, I need to know, do I evacuate people to the Beta site or not?”
“Elizabeth, I don’t know. At the moment, it doesn’t appear whatever is going on in that room is building toward an explosion, but something is happening.”
Lorne leaned forward, “Doctor McKay that's not an answer.”
“That’s all I have, maj…”
Chuck’s urgent voice over their COMs silenced McKay. ”Dr. Weir, SGA-9 was scheduled to return from their mission at this time. The gate engaged then shut down; we no longer have power to the gate.”
McKay was already out the conference room door, Lorne hot on his heels. When they reached Chuck’s station and the DHD console, McKay shoved Chuck’s chair out of his way. Lorne grabbed the young lieutenant before he fell onto the deck.
McKay scanned the Ancient data display, pounding on several of the crystals, then turned to his laptop. After a couple of minutes, he looked at Chuck, “What did you do?”
“Nothing we don’t always do, Dr. McKay. SGA-9 was scheduled to dial in at 1100; they left at 0900 to take medical supplies to PS4-118, with plans to return in two hours. The gate engaged on time then went dark.”
“Rodney,” Elizabeth asked quietly, “what’s happened?”
“The only system that is affected is the power conduit to the stargate.”
“Why did it shut down?”
Zelenka cleared his throat, looking up from his laptop, “I can answer that, a power surge entered the gate’s power source seconds after the gate engaged. It originated in the building on the West Pier.”
“How many teams are out?”
Lorne replied, “Two; SGA-3 is at the Beta-site. Dr. Weir, both teams should be safe for the short run.”
“Well, there’s that.” Weir turned to McKay, “Rodney, figure this out, before it gets worse.”
~ooOoo~
Beckett sat next to Sheppard’s bed, pouring over the colonel’s latest tests. He insisted that Teyla and Ronon take a break, finally convincing them that he would remain with Sheppard while they had a hot meal.
Closing his eyes, he went over the test results in his head. Sheppard was improved; the cranial pressure had dropped, and the scanner showed only one electrical pattern on the EEG. What puzzled him was the fact Sheppard was exhibiting neural impulses in a section of his brain where humans were normally dormant.
“Carson, you awake?”
“Ah, Elizabeth, come sit down.”
“Where are Teyla and Ronon?”
“I convinced them to have dinner and rest for a while.” He chuckled, “Which means they left about fifteen minutes ago…they’ll be back shortly.”
Elizabeth laughed softly, as she brushed her hair behind her ear, “Yes they will. How is he?”
“Resting better, pressures down and there is much less activity going on in there.”
“I hear some hesitation in your voice, what are you not telling me?”
He turned his view screen for her to see, “The second pattern is gone, but these wiggles right here represent activity in an area …uh… humans don't have activity.”
Sucking in a deep breath, she replied, “Are you saying that whatever entered John’s brain has altered it?”
“Yes, I am…whether it’s a permanent change or simply residual current from the other pattern, it’s too early to tell. I do think from the results of these latest tests he’s going to wake up soon.”
“At least, there is some good news, we’re not making much progress in determining what’s happening.” Weir was updating Beckett on the science team’s efforts when Ronon and Teyla returned, quickly recapping for them.
Teyla shivered, “You are telling us, Dr. Weir, that Rodney has made no progress.”
“Yes, in simple terms, we know nothing more than we did when the alarm sounded. I…”
Ronon stopped her, “He’s moving.”
Beckett jumped up and leaned over the colonel, “John, can you hear me?” He gently shook Sheppard’s shoulder, “John…wake up.” Sheppard's eyes fluttered open slightly; he tried to speak but his voice was weak.
“It’s okay, laddie, just rest. It’s good enough that you are awake, even for a few minutes.”
Turning to call for the nurse, Beckett stopped when Sheppard grasped his arm. His voice feeble, the colonel murmured, “A-At…lantis…dan…ger.”
Sheppard had fallen back into a deep sleep by the time McKay arrived in the infirmary. As he blustered into the private room, Teyla shushed him.
“Rodney, please be quiet, John is asleep.”
“What did he say…Atlantis is in danger? Wake him up.”
Weir answered, “Yes, he said Atlantis is in danger, and no... we are not waking him.”
“What kind of danger? What else did he say?”
‘Nothing else, Rodney; he’s very weak, but Carson thinks he will begin to wake up for longer periods. We’ll find out what he meant then.”
“We need to know…I just got word that the power levels are increasing in that room, and we are beginning to lose power in some areas of the city.”
Weir stood up, “When did this start?”
“As of fifteen minutes ago, the power drainage remained slight, predominantly in areas that we don’t access often. Elizabeth, we need Sheppard to figure out what’s going on.”
~ooOoo~
Sheppard noticed the aroma of coffee first, then the smell of antiseptic and the flowery detergent the laundry used to wash the sheets. Surprisingly, he felt comfort rather than distress; he was in the infirmary, and this had to be real.
He struggled to open his eyes, managing only narrow slits to start with. The coffee aroma along with the sound of faint tapping could only mean one thing; McKay was nearby.
“McK-ay…coffee….”
A yelp of surprise and the sound of something striking the floor was quickly followed by McKay’s voice “Sheppard... you’re awake.”
“Yeah…coffee…h-head hurts…”
“I’ll be back, going to get Beckett.”
McKay rushed from the room, and Sheppard heard him contact Elizabeth before his voice faded away. His vision was clearing and he gazed around, realizing he was in one of the trauma rooms.
“Crap,” he whispered, “must be bad.” Woozy, he lost track of time until he heard Beckett’s soothing brogue.
“John, you still awake?”
Sheppard slowly opened his eyes, “Uh huh…head…hurts.”
“No doubt, laddie; you fell into one of the rafts in the canal, hit your head on a motor. But you’re gonna be fine, just need to rest.” Beckett whispered quietly to the nurse, then continued, “I’m going to give you something for the pain, and let you sleep.”
“C-coffee…”
“I promise you can have a cuppa when you wake up, now you need to sleep.” Beckett turned to watch as the nurse injected pain medication into the IV port, when Sheppard grabbed his arm.
“No…n-need to wake...up…At-lantis…in trouble…”
“How do you know?”
“T-told me,” Sheppard’s voice trailed off as he drifted to sleep.
Six hours later, as Weir approached the conference room, the sound of McKay and Zelenka’s bickering drifted through the doors. She sucked in a deep breath and entered.
“So, I’m assuming you two haven’t figured out what’s going on.”
McKay looked up quickly, “What makes you think that?”
“Do you?”
“Uh…no, we don’t. Zelenka hasn’t been able to decipher any of the data we’re receiving.”
Glowering at McKay, Zelenka spoke, “What we do know, Dr. Weir, is that the power drain continues, but at a slow pace.”
“Where have we lost power, besides to the gate?”
“Currently, power loss is confined to the uninhabited sections of the city, but the outages beginning to affect some of the Ancient equipment. We have shut down as much equipment as we can and still maintain citywide sensors.”
McKay added, “The energy signal coming from that room has remained steady for the last several hours. There is no question that the outages are a result of the energy surges coming from that room.”
“Doctors, we need answers.”
“What we need is Sheppard; did he wake up again?”
Weir shook her head, “Not yet, but Carson says his brain scans are more stable. At the moment, he’s sleeping and Carson refuses to wake him up.” She pursed her lips, “Do you have any idea what John meant when he said someone told him that Atlantis was in danger?”
“Not a clue…unless whatever alien was inside his head told him.”
“Rodney, do you really think there was an alien entity in John’s head?”
“After what we’ve seen these last two years, I’d believe just about anything.”
“But from where, how…” Weir stopped, listening to her COM. She stood up, “That was Beckett, John’s waking up. Maybe we can now find out what he meant.” Weir and McKay headed for the infirmary.
~ooOoo~
The thick fog swirling in his head was slowly lifting. Opening his eyes, Sheppard first thought there were dark shadows on the walls, but as his vision cleared, he realized it was Ronon and Beckett.
“Hey…”
Ronon spun around, “Sheppard...
“Yeah…t-think it’s…me.” He struggled to sit up, but Ronon held him down. “Oh…okay, I’ll just stay h-here.”
“Aye, laddie, exactly what you should do.” Beckett appeared at Sheppard’s bedside, “Now, how do you feel?”
Sheppard scoffed, “Not great…but I need to get out of here.”
“You are doing no such thing; you have had a serious injury and….”
“N-No… gotta get up.” Sheppard again attempted to sit up, but Ronon’s hand on his shoulder stopped him. Sighing deeply, and his voice weak, “You don’t understand, I have to get up.”
Weir and McKay arrived, and Weir asked, “Why do you need to get up?”
“A-Atlantis…in trouble…”
“How do you know that there’s a problem on Atlantis? Did you hear the alarm?”
“Alarm…I…think maybe…sharp pain in my head…woke up…h-here.” Sheppard tried to sit up again, and this time Beckett helped him by raising the head of the bed.
Weir asked, “John, Dr. Beckett said someone told you Atlantis is in danger.”
Sheppard dropped his head, reluctant to answer her fully, “Someone…did.”
Beckett interjected, “You’ve been having headaches for several days, haven’t you?” Sheppard nodded and Beckett continued, “Your initial brain scans showed enormous activity, there were two separate patterns at one time, and now…”
“Now?”
“Now, whatever was inside you has vanished, but…it left you with areas of your brain more developed than before.”
Sheppard gave Beckett a faint half-smile, “She…said she had to rewire me…to help her.”
Weir asked, “Who had to ‘rewire’ you?”
Quietly, he answered, “Atlantis.”
McKay blurted, “Atlantis? What do you mean Atlantis told you?”
Sheppard rubbed his forehead, “She can…talk to me…” he grimaced dropping his head.
Beckett lowered the bed, “Alright, everyone out. I’m giving him something for the pain, and then he needs to rest.”
Weir, McKay, along with Teyla and Ronon stepped into the main infirmary ward, all noticeably shaken. Teyla spoke first, “Could John really be talking to Atlantis?”
Weir shrugged, “We know he can control Ancient equipment better than anyone, I…” she stopped, turning to McKay, “Is it possible that the gene would allow Atlantis’ computer core to communicate with him?”
“The brain generates electricity; the computer core is powered by electricity generated by the Zed PM. I suppose it’s possible; the gene may provide receptors to accept signals from the core.” He paused, then added, a note of skepticism in his voice, “It could be conceivable...maybe."
Teyla asked, “He said ‘she’; was he referring to Atlantis the same way as you refer to the jumpers, as female?
McKay sighed, “Could be, but knowing Sheppard’s luck with Ancient women Atlantis probably is a girl.”
Weir returned to her office a few hours later, after an unsuccessful attempt at getting some sleep. Grabbing a cup of coffee, she reviewed the reports coming in from Lorne. The major was overseeing the scientists who were attempting to enter the mysterious room. Beckett agreed to try to open the door once he was satisfied that Sheppard was resting comfortably, but Lorne reported Beckett failed as well.
Leaning back in her chair, Weir closed her eyes, resting her hands on her forehead. She nearly fell from her chair when the self-destruct alarm shattered the quiet. Jumping to her feet, she dashed into the control room, where Lian, the night gate tech was typing furiously on his keyboard.
“What’s caused the self-destruct to engage?”
Lian shook his head, “I don’t know, Dr. Weir. I’ve started running a diagnostic, but nothing appears to be out of the ordinary.”
She tapped her COM, “McKay, get to the control room now.”
~ooOoo~
“Colonel Sheppard, can you hear me?”
Sheppard struggled to comprehend, “Atlantis?”
“I need your assistance; the ark is awakening.”
“The ark…what’s…the ark?”
“I will explain, but you must be conscious to assist me. I need to finish creating the neural pathway for you to fully interact with me. It will take both of us to stop the ark.”
“What do I need to do?”
“Allow me to guide to you, open your mind.”
Sheppard felt a warmth flood through his body and began to wake.
Carson Beckett was asleep on a cot, stashed in his small office, only a few steps from Sheppard’s private room. Once the colonel was sleeping soundly, Beckett finally convinced Ronon and Teyla to rest in their quarters. They agreed but only after he assured them he would stay in the infirmary. After they departed, Beckett told the night nurse, he never promised them he wasn’t going to sleep as well.
He was snoring lightly when the self-destruct alarm sounded. Waking abruptly, he was getting up as Leigh opened the door, “Dr. Beckett, its Colonel Sheppard. I just checked on him; he's not in the infirmary.”
Beckett brushed past the nurse as he tapped on his COM, his voice gruff, “Lorne, Beckett here…Colonel Sheppard has left the infirmary without authorization. I need you to find him.”
~ooOoo~
Thankful that he knew the city’s layout better than anyone, Sheppard took back corridors to reach his quarters. The door opened silently and Sheppard slipped inside, confident he had not been seen. Stripping off the infirmary scrubs, he grabbed a pair of track pants, a t-shirt, and a hoodie and dressed. As he sat down to put on his running shoes, he felt a now recognizable sensation enter his consciousness…Atlantis.
“You’re here.”
“Very good, you can now sense as I join with you.”
“Join…? Oh...okay…” Sheppard shuddered slightly, as a wave of pain passed through his head. “Uh, you need to tell me what’s…happening, the self-destruct just sounded. What…kind of danger are we in?”
“In less than four hours, I will be destroyed.”
Sheppard felt the flush of adrenaline spread through his body, but his voice, although weak, remained calm, “Then we need to get started, but first I need to get out of here. They’ll be looking for me.”
Atlantis directed him through little-used corridors, twice preventing him from being intercepted by Marines searching for him. She led him to an area the expedition had yet to explore, a small chamber in on the North pier, three decks below the water line. The chamber contained an Ancient console, a conference table, and several familiar white couches. The console and the light towers began to glow as Sheppard entered.
“Where are we?” Sheppard asked as he sat down on the nearest couch, exhausted from the trek.
“This is an auxiliary control center for the sensors located on the hull. During space flight, if the control tower was otherwise engaged, technicians would use this console to monitor the sensors for anomalies.”
“Otherwise engaged? Do you mean on a scientific mission or in combat?”
“You suspect my history extends far beyond the difficulties with the Wraith, and you would be correct. I was built for scientific exploration and as a means to spread humanity across the vastness of space. Along the way, there were many encounters, and I will provide all of that information to you in due time. I need for you to allow me access to your mind; if you do not resist it will not be as painful. I have nearly completed the neural pathway allowing us to communicate freely.”
Sheppard swallowed deeply; his head hurt badly enough, but he had to risk allowing Atlantis to finish her task. “What do I need to do?”
“I suggest you lie down and relax; this will not take long.”
Grimacing as Atlantis deepened their connection, he was relieved the pain was less intense as she had promised. The normal background hum of the city he sensed from the moment he first emerged through the gate was becoming stronger. Sheppard felt connected to Atlantis from the beginning and when he traveled off world or to the mainland, he felt uneasy, as if part of him had been left behind. When the Ancients returned only a few months before and reclaimed the city, he felt lost during the month on Earth and joyous when they retook Atlantis from the Replicators. Aware he should have been dismayed the Replicators murdered the Ancients, knowing what secrets the builders of the city possessed, he had instead been elated they could return to the place he felt at home.
As his thoughts drifted to the days after returning to Atlantis, Sheppard lost track of time. He was startled when he heard the soft voice in his head calling his name.
“John, can you hear me?”
“Yes, sorry…I was thinking about something…” A wave of panic crept into his throat, “Can…can you tell what...I’m thinking?”
“No, I am unable to read your thoughts, only to communicate when you accept my entry. I can perceive your emotions. My creator believed that the artificial intelligence processors should be capable of more than operating the cityships. He rewrote the code to include the ability for the processors to interact with someone who possessed an extremely strong gene.”
Sheppard exhaled deeply, reassured Atlantis wasn’t telepathic. He noticed her voice was stronger, richer, as though she was standing beside him. “Are you done?”
“I have completed the procedure of stimulating the dormant neural paths within your brain. It will take time for you to understand how to utilize your new capabilities. At this time, it is imperative that I be able to communicate with you. I cannot stop what is occurring, but I can convey what needs to be done to you.”
“What do you need for me to do?”
“I believe the place to start is for you to understand why we can communicate. My creator left a file as an explanation for my muses. Please relax and open your mind.”
Sheppard closed his eyes. In the darkness, a faint light appeared, then morphed into an image of a tall, lean man sitting before a bank of consoles, much like those on Atlantis. His dark hair, patrician features, and serious gray eyes gave the man an aura of distinction. When he spoke, his voice was deep, commanding.
“I am Adalricus Ludo, a member of the Alteran Science Praeclarum. I realize you have many questions, most of which can be answered by Atlantis. I will only give you a brief overview of the cityships and the Artificial Intelligence Processor residing on the ships, in particular, the AIP on this ship.
Artificial Intelligence Processor1187719-07, holds the designation Atlantis. She is one of seven cityships built to soar among the stars, bringing life to barren worlds, and knowledge to existing worlds. Atlantis was built on Altera Seven, one of seven worlds the original Alterans colonized as they spread across space. A cityship was built on each world to carry the Altarens’ message.”
Ludo stood up and walked toward a monitor displaying a schematic of a cityship. “The AI processors were designed to be the operating systems of the cityships. I realized that it was one thing to be able to sense the need to open a door, raise a shield, or engage the stardrive. I also realized that the cityships would most likely never return to their home worlds. I believed that the AIs needed the ability to learn, to grow, to understand humans, their emotions, their fears, their joys. I wanted them to interact on a level that the Alterans had never been able to accomplish before.”
Hesitating for a moment, he gazed at the monitor, then continued, “I knew many of my colleagues, and the Alteran Council would vehemently disapprove of my plan; they valued logic and science over emotion. Covertly, I rewrote the code giving the AIs the ability to respond to the person who possessed the strongest ability to interact with the technology. All Alterans could sense the technology due to the gene they possessed, the gene that responds to the frequencies created by the crystal-based systems. However, only a minority of Alterans possessed a gene strong enough to interact with the code I embedded. That person, muse, would be able to hear and converse with the AI, who, in turn, would learn from their muse.”
Ludo paused again, “I will most likely never know the outcome of my actions. I only hope muse and AI grow and learn together. If you are viewing this message, then you possess the gene capable of interacting with the AI. Please use your ability wisely and remember the purpose of the cityship, to gain and spread knowledge.”
Ludo’s image faded from his consciousness, and Sheppard opened his eyes. In the dim light, his eyes fell to the console in the middle of the room. Ludo could have been standing in that spot when he recorded his message. He was overwhelmed with the realization, of how much they didn’t know about the Alterans. There was a great deal he wanted to ask Atlantis but now was not the time. He sat up slowly, dizzy, his head pounding.
“Atlantis, what’s the danger from?”
“Several thousand years ago, I was directed to a region called the Galleré. The Galleré formed a passageway between two massive nebulas in an area rich with young solar systems. The leaders of the city spent many generations there, over two thousand years, seeding suitable planets, exploring the nebulas. Much was learned during that time, but one day, a shuttle returned from a mission with news of a planet where humanoid life had developed independently. There was much excitement, and against the wishes of many of the governing council, the Administrator ordered a return mission, this time not cloaking the shuttle but initiating contact.”
“I take the contact didn’t go well.”
“You are correct; it did not. There was no confrontation but the contact lead to dissidence. The humanoids called themselves the Iriki. They lived alone with only the nebulas in the sky for companionship, peaceful people, with no technology, an agrarian society. They were curious about the city, not frightened at all. In their usual manner, the Altarens offered their expertise to improve their crops, their dwellings, introducing them to technology. The Iriki resisted. They decided that our technology was not for them and asked the Altarens to leave.”
“Did the Altarens refuse?”
“No, they adhered to the Irikis wishes and did not contact them again, although that was not the last heard of the Iriki philosophy. As the weeks and months passed, it became clear that a group of Altarens, who knew no other existence than living on Atlantis had been influenced by the simplicity of the Iriki lifestyle. They chose to turn away from technology and begged the Administrator to return them to Iriki, so they could live out their lives on the planet. The Administrator refused, which made the dispirited Alterans even more dispirited. I was directed to depart from the area a few months later, contact with the Iriki all but forgotten.”
Sheppard dropped his head onto the back cushion, closing his eyes, “Forgotten by everyone but the ones who wanted to stay behind.”
“Yes, you are correct; they were determined to change the Alteran philosophy, regardless of the amount of time it would take. The dissidents were very careful, their actions unknown. The members of The Order of Libét as it was later learned they called themselves, remained secretive, hiding their members and numbers from the others. The Order of the Libét remained undetected until thousands of years later when the Alterans, faced with defeat by the Wraith, decided to abandon the city.”
“How did they find out?”
“Members of the Libét volunteered to be part of the advance scout team, returning to Earth to assess the conditions and determine where the population would settle. They followed through with their responsibilities and located suitable areas for habitation. Departure schedules were created, but one night prior to the exodus two hundred and seventy-three people gated off the city covertly never to be heard from again.”
“That’s a lot of people, no one noticed?”
“As now, there were few technicians on duty during the night hours, and they disappeared also. With so much to do, the city leaders chose to ignore their departure and turned to other tasks. There was much activity; the scientists were busy copying data from my storage banks to take with them. Their hope was to return someday and wanted the data preserved.”
“Atlantis, why are you taking time to tell me this…don’t we need to stop this ark thing?”
“Yes, and we now have three hours to do so, but it is important that you know what occurred. Only a short time before your Administrator arrived…”
“Elizabeth?”
“Yes, just before she arrived, a scientist discovered an encrypted file embedded in my central core and notified the man you know as Janus. He became intrigued and worked feverishly to open the data. He accomplished his task, and discovered what the Libét had done.”
Sheppard was surprised that Atlantis seemed to pause for dramatic effect; she definitely adapted human behavior. “What had they done?”
“Do not forget the members of the order were Alterans, and they continued to live here. Many members became scientists to acquire the skills to accomplish their goal. They may have abhorred technology, but they employed it in a plot to destroy the city. Plans they had formulated many, many years prior, waiting for the opportunity to destroy the cityship, were initiated when the decision was made to abandon the city. Plans to be activated should the Alterans return.”
“I’m assuming that the alarm that sounded was because of the Libét, but why?”
“When I began to assist you in developing your ability to use the gene, they discovered you. As you grew stronger, the sensors put in place began to notice you; when you were identified as a muse, the Ark was activated. I sounded the alarm in an attempt to warn you of the danger.”
“This ark, is it a bomb?”
“It is an incendiary device and you are the detonator.”