I really like Altair and the story of the first Assassin's Creed game. The plot itself is pretty repetitive and the big twist is predictable but I came across the game at a time when I was just starting to become an atheist and the themes within the game really connected with me and fascinated me.
In a sense Altair starts out as an atheist (at least one of the first things we see him do is ridicule the idea of the Ark of the Covenant, which turns out to be real but not because of divinity). But if Al Mualim is seen as a metaphor for religion then the story is clearly about becoming an atheist. In the beginning Altair alternates between reckless arrogance (thinking he can take Robert de Sable on his own) and blind faith (risking death by taking a literal leap of faith just to prove Al Mualim's point about how dedicated his soldiers are). Each of the nine Templars he assassinates manages to shake his worldview with their dying words, usually along the "we're not so different" line of though, exposing him to alternative points of view for the first time. Though he's unsure how to handle these challenges to the beliefs he was raised in, he implicitly trusts his master to hand him the resolution to any cognitive dissonance and at first is mostly satisfied with Al Mualim's answers, but as the game goes further he grows frustrated with contradictions ("You speak in circles, Master. You commend me for being aware, then ask me not to be. Which is it?"). The Assassin philosophy (as portrayed in the game) is ostensibly one of enlightenment through reason and skepticism, as illustrated in this wonderful exchange:
Al Mualim: Before you go, I have a question for you.
Altaïr: Of course.
Al Mualim: What is the Truth?
Altaïr: We place faith in ourselves; we see the world the way it really is, and hope that, one day, all mankind might see the same.
Al Mualim: What is the world, then?
Altaïr: An illusion. One which we can either submit to; as most do, or transcend.
Al Mualim: What is it to transcend?
Altaïr: To recognize nothing is true, and everything is permitted. That laws arise, not from divinity, but reason. I understand now that our creed does not command us to be free; it commands us to be wise.
Al Mualim: Do you see now why the Templars are a threat?
Altaïr: [Understandingly] Where as we would dispel the illusion; they would use it to rule.
And this is the philosophy Altair accepts (and comes to understand more deeply throughout his journey). But what he gradually realizes is that there is an inherent contradiction between that ideal and the way he is expected to unquestioningly serve Al Mualim. In the end Altair realizes Al Mualim is at bottom no different than the Templars (in fact, he
is and ex-Templar) and that his own loyalty lies with the Assassin's creed itself (and only those parts that are true to the spirit of the above conversation) rather than the Order or its master. In other words, the abstract ideals of morality are liberated from their ties to concrete religious institutions. Finally, in the game's climax Altair stands in open defiance of his former master. Their final confrontation is probably one of my favorite cutscenes in video game history. Good stuff starts at 3:14.
https://www.youtube.com/watch?v=Fod7b7_pT90And that's how his story ends. Al Mualim is dead and we killed him. And now Altair has to decide what to do on his own with more questions facing him than ever. Good for him.
tl;dr: Altair's transformation parallels the experience of many people who become atheists. Also I really like this game.