Slow burn K/S fic set after ST reboot, before STID, at the SF Academy and during the Mission
Hiya! I have been looking for a particular slow-burn K/S fic for over a year now without any luck. The fic starts just after the end of the 2009 reboot film. In it, the Enterprise crew is back at the Star Fleet Academy to help Star Fleet get back on its feet. The Admirals, Pike in particular, believe that the best thing is for Kirk (and the rest of the crew) to command the Enterprise's 2 or 5 year-long mission. However, as Kirk is still quite young etc. they ask Spock to spy and investigate him to see whether he has what it takes to be the Captain of the Enterprise for the foreseeable future. At first, Spock is very skeptical about it, but he agrees to shadow Kirk for about a year, and they slowly become friends. Kirk becomes more and more interested in Spock as he has read up on him and has realized how awesome he is. Meanwhile, Kirk has told the Admirals that he wants to help Star Fleet and the Academy in any way he can, which leads him to get involved in a very creepy and dangerous part of Star Fleet, which deals with infiltration and espionage, sort of like the CIA or FBI. Kirk has to wear a special black suit. As the missions grow more dangerous, shady and corrupt, Kirk tries to back out, but is not able to, as the leader of the group is an Admiral and will kick Kirk out of Star Fleet if he doesn't help him. At one point Kirk gets really beaten up and McCoy, Admiral Pike, and Spock get really worried about him. This happens the day before Kirk has to take the final Captain exam (not the Kobayashi Maru). Kirk is beaten up so bad that Pike has to move the exam. At first, Spock thinks Kirk is missing his exam on purpose, but gets really worried when Pike and McCoy has told him what has happened.
After the Enterprise has finished being repaired, Spock finally agrees that Kirk as well as the other crew members should command the Enterprise. The first thing Kirk does when he gets notified that he's the Captain is to ask for Spock to be his First Officer, and he does not want anyone else. However, Spock is still unsure whether he should join the Enterprise. This is in part due to him wanting to help New Vulcan, but also because he does not like Spock Prime's interfering with his business. Spock agrees just in time and the Enterprise starts its mission.
However, the dangerous group is still in touch with Kirk he goes on a last mission for them. While doing the mission, Kirk and Spock come up with a plan to get rid of the group's leader, which I think might have been one of the other Admirals (though not Marcus, I think it was a woman). In the last mission, Kirk (and Spock) have to steal a special stone or diamond. The group leader wants it to blackmail the planet into becoming a member of Star Fleet. After they steal the diamond, they realize that the diamond is actually a spiritual nature energy creature. While aboard the Enterprise, the creature tells them that it was its home planet's God or spirit and that when it is taken away, the planet it came from will die. Being a telepathic creature, it can sense Spock and Kirk's T'hy'la bond and talks about them as if they are one and the same creature. Spock befriends it and he and Kirk decides that it needs to be taken back to its planet. As they do this, they are also able to get proof of the shady and dangerous Star Fleet group leader's evil doings, and the group leader is incarcerated. After this happens, the other group members decide that they want revenge for what Kirk has done. They do this by wanting to hurt or kill the most precious thing that Kirk has. Kirk is oblivious to this and thinks they are going to kill him or the Enterprise. He realizes too late that it is Spock that they want to kill, and Spock is shot in the chest with a fazer set to kill. As Kirk thinks Spock has died, he wants to kill the rest of the dangerous group. Of course, Spock didn't die, as a Vulcan's heart is located in the stomach, next to the kidneys, and not in the chest. Spock is able to find Kirk and calms him down by expressing his love for him and they make love.
That is all that I remember. I am sorry that I don't remember the name of the dangerous group or the planet where the creature is from. If I did, I might've found it already. I hope you're able to find it for me.
PS: I don't think Star Trek Into Darkness happens at all in this fic.