Canon Update Information.
Updated Personality:
In the four years since season 1, Allelujah grew a lot as a person- and not always in a more mature fashion. He still retains his kind, polite, and generally friendly manner with people on the surface- he listens, he still prefers to keep his own troubles personal and not a burden to others, and he's still very unsocialized. Allelujah is still quiet, but will speak his mind if need be. He won't hide his opinion, but if it reasoning or his troubles are personal, he won't often confide them in others unless he trusts them.
However, without Hallelujah to keep him in check, Allelujah must do things on his own. While Allelujah isn't "stronger" in this per se, he's more aware of his own responsibility, knowing that he must take action if he wants things done. This is both a good and a bad thing. It's good that he's finally able to step up and get shit done, able to "pull the trigger" in a way, but bad in that he needs to learn self-restraint when his emotions get ahead of his logic. One such example is when he vows to himself to save Marie-- Upon seeing her in battle, he grabs at her mobile suit and brings Arios and her custom A-Head crashing down on an island, a move that could easily get them killed, as explosive as mobile suits seem to be.
His selfish and stubborn side also tends to show a bit more, especially when it comes to Marie. He wants to save her, he wants to take her away, and because he thinks that's the best, he believes that everyone should think that's the best.
Of course Allelujah won't be as insanely intent on everything as he is with Marie-- but it can still show up, even if it's moderately subdued. If he believes something, and honestly finds reason to believe it, he believes it is the correct thing and that others should agree. He doesn't have Hallelujah to tell him how hypocritical his kindness and thinking is, and without that check, occasionally when set on something he could go a bit overboard.
The element that's mostly affected his personality, though, was four years spent in solitary confinement. As he stated in an episode "I just wanted to let myself rot away." For four years, Allelujah lost every meaning to his life he had, and believed everyone he had once known to be dead, except one. Because of this, he can be a bit distant, but at the same time, not terribly fond of silence. Being rescued, however, and finally coming to terms with Marie has mostly placed that part of his past behind him-- though he still has 'sins' to atone for, such as the near-genocide of his brethren at the SSO, and though Celestial Being still must continue, he can at least be secure in his personal life.
Due to this, while he'll still be longing for Marie, there won't be that sense of urgent desperation that comes from longing to find her and take her away, and there won't be that embitterment about Marie wishing to fight. While she's still very important to him, he can be secure in knowing he's gotten his "happy ending."
Update point: Season 2, Episode 8
Since we last left Allelujah, with a grave head injury and Hallelujah ditching him, Allelujah managed to eject the Solar Furnace from Kyrios Gundam (later picked up by Fon Spark, who ditched Alle,) and was later picked up by the UN forces and taken as a prisoner of war. In the series, Allelujah says very little about his stay in the federal prison, though official files and the novels state that there was torture involved and he was kept in solitary confinement for all four years.
Very little changed over the years, until one day a new Lieutenant in the A-Laws (The Autonomous Peacekeeping Military force of the Earth Sphere federation, separate from the ESF Army) joined the interrogation. Lt. Soma Peries was chosen to helpfor her ability to use Quantum brainwaves, though she immediately noted that she detected none from "E-0057", aka Allelujah. Upon sighting her, Allelujah is overjoyed, able to do little but repeat her name and protest that she is, in fact, Marie Parfacy, the child she grew up with. Soma thinks he's just crazy, and then leaves.
Around this time, Celestial Being is finally getting off their ass to help him, and so they do- Things are crashed into other things, Setsuna tosses Alle directions and tells him to find his Gundam, and they leave him to figure shit out on his own. He immediately sprints off to where Setsuna indicated, only to run into-- you guessed it-- Soma Peries. Allelujah assures her once more that she is Marie Parfacy, his childhood friend. Something about this triggers Soma and she collapses as faint memories come flooding back, though before he can rush to her, reinforcements show up.
So Allelujah hops in his Gundam and gtfo's, vowing that he'll come back and rescue her. So he arrives back on the Ptolemy, is given coffee, and sat down. Amazingly, for a POW for four years, Allelujah seems to cope with returning fairly decently-- the appearance of Lyle, Lockon Stratos's twin brother- is a little disorienting, but he deals with it with the help of Tieria's joking.
The next time we see Allelujah, the Ptolemaious is still evading A-Laws detection, and he goes to visit tactical forecaster Sumeragi Lee Noreiga, who's being super emo. He brings her wine, asks if she'd care to share a drink, and they talk. He confides in her about SoMarie and his stay in prison, explaining that she was his childhood friend, they bore a unique connection with their quantum brainwaves, and that he wants nothing more than to save her from being forced to fight. Sumeragi tells him that she envies him for finding a reason to fight, to which he responds. "I believe you have reason to fight. if not, then why did you rescue me? If it's you, I'm sure you'll be able to discover your own reason for fighting."
While he's on this super roll of purpose and the like, he goes to visit his Gundam, promising to himself that he'll use it to save Marie- even without Hallelujah, even without his Quantum brainwaves-- and then it cuts off for more Tieria. WTG, S2.
Anyway, so CB is taking Pricness Marina (Who Setsuna ditched Alle to go save back in the prison) to take her back to her country where she belongs. On the way they're ambushed by a Mobile Armor called the trilobite and shitsucks, since they're underwater. A fight ensues, and Allelujah really doesn't do much in it. Setsuna fights Mr. Bushido, and that's kind of cool, but not really our focus. Soma launches in her Mobile Suit and beats the shit out of Allelujah in Arios, before being driven away by Kataron forces Which is a little Plot stupid, because she could kill them all, but hey, whatev.)
So Kataron (The anti-federation rebels) takes the princess back, and CB chills out for a bit-- though Kataron doesn't really trust CB, they sort of have to try. Saji's a little bitch and tries to run away and is picked up by the ESF Army, though Colonel Sergei Smirnov lets him go-- but not before a subordinate alerts the A-Laws. A-laws show up and bomb the fuck out of everything and it's sad, but Allelujah really isn't involved with that, or with Ali Al-Saachez burning Azadistan the fuck down.
In fact, the next time he's really involved with anything is a battle after Sumeragi passes out, so she's not there to do all the tactical stuff. It's another fight with the A-Laws in which he's able to recognize Soma's Mobile suit, and like the desperate sack he is, he tackles her mobile suit with his and they both go tumbling down to and island, something that really should have killed them both. When Allelujah awakes he immediately goes to make sure she's alright, and like the good, trained soldier she is, she attacks the fuck out of him.
While tackling him, though, she gets a surge of some kind of QBW stuff and passes out. Later, she awakens as Marie. Allelujah returns from checking out the Mobile Suits and confirms that systems are down, and they're trapped their until help arrives-- from either side. He asks hwer why she became Soma Peries, and she mentioned that the SSO implanted another personality into her to regain the senses that she had lost as a child-- but that she was happy, a snow she could see him. He affirms that he's happy as well, never imagining that they'd be able to speak normally and not with QBW telepathy.
Allelujah tells her all about how he escaped and murdered his friends. Even though she seems forgiving, he admits "I have no excuses. I am Hallelujah. As the only survivor, I cursed them; the SSO, the world... that's why I became a Gundam Meister; to change the world. Because all a super soldier can do is fight." He finally shows an awareness that he and Hallelujah were/are, in fact, the same person, desires and motives coinciding.
He admits to destroying the SSo, she admits to killing Hallelujah, there's some awkward bonding. he tells her that she was all he could think of, and he wanted to save her-- but not that he had, he wasn't sure what to do. (Way to fail, Alle.) She admits that she's thankful for him and that she isn't a tube girl anymore, etc, its touching and stuff.
A little into their reunion, though, Sergei Smirnov of the ESF Army finds them, threatening to kill Allelujah. Eventually, though, he decides that Marie may make her own decisions, and states that he will report her as KIA-- though he makes Allelujah promise that he'll keep her safe.
Then there's some stuff about Tieria coming out about being an innovator, the boobies dress, and yeah, but that's pretty much it- happy at home with his waifu.
Physical Changes
Allelujah hasn't changed much over the past four years other than "growing up", per se. He's gained a scar over his right eye that's generally obscured by hair, though now his hair is shorter and parted to allow both eyes to show.
His facial features have grown more angular, with a bit more of a square jaw (Compare: One, Two) but a lot of that is simply from lost weight from the four years of prison.
He's still the same height, but perhaps a smidgen broader and more grown up (But that could just be the design of the S2 Uniforms.)
Other than that, he's the same old guy.