A series of events led him and others to be left adrift in space, and out of survival the darker half took over and killed all on board. It is possible this is when Allelujah was discovered by Celestial Being.
Like all of the other Gundam Meisters, he was selected by Veda to be a Meister, and maintains this position (evidence in episode 5 when he abandon his mission to rescue a group of civilians).
When Setsuna starts a war with the Trinity siblings, Allelujah stayed behind to look after Ptolemy in case anything unexpected happens, which in turn makes him the only Meister to have never fought against the Thrones/Trinities.
During the final battle against the UN forces, Allelujah manages to destroy a number of the GN-X before been outpowered by the powerful Alvatore, which manage to heavily damaged Kyrios in the process. Allelujah then battles Soma and Sergei and manages to damage Sergei's GN-X but he retreats when he realizes he knows Soma, and he calls her 'Marie'.
He seems to know Soma Peries from his days as a Super Soldier experiment, calling her by the name "Marie".
Like the other Gundam Meisters, he is not shown in the epilogue of episode 25.
There are two halves of Allelujah's personality due to the enhancing of his brain. The two halves differentiate by the calling of the darker half, 'Hallelujah' as well as Allelujah's hair covering the left half of his face to reveal a gold coloured right eye.
The dominant personality is Allelujah, a decidedly kind and gentle person. When the rest of the Ptolemaios crew went to Earth, he chose to stay and help with maintenance. He doesn’t like to kill, and it often brings up a confrontation with his other half, such as when he was about to fire upon the HRL’s Super Soldier Facility. He is against killing and was strongly opposed to when La Eden began attacking civilians.
Hallelujah on the other hand carries a strong survivalist view, kill or be killed. He will do anything in order to survive. When Allelujah is in conflict over what he should do, Hallelujah will offer to 'take over' Allelujah's body so he won't be so morally conflicted. Hallelujah has gone as far as to claim he is the embodiment of Allelujah's desires, taking action when Allelujah's morals get in the way.
Hallelujah also has the ability to block out interference from other people who were used in the HRL's experiments, relieving Allelujah of severe pain induced from it.
Allelujah and Hallelujah can combine. This is what Allelujah/Hallelujah calls the "perfect soldier" - a mixture of the planning and thinking done by Allelujah with the instinctive battle sense of Hallelujah. When fully combined (ie, when Allelujah is strongly willing to fight), Allelujah/Hallelujah raises his hair up so that both eyes are uncovered and their skills are improved by a vast amount.