outcome
Altaïr kills Al Mualim, keeps the Apple and sees a map of other artifacts. Desmond survives Abstergo's attempt to kill him thanks to Lucy. Desmond finds blood drawings on his wall that warn of a future catastrophe.
Assassin's Creed
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Every ending, what changes it and what it means.
Assassin's Creed ends with Altaïr's discovery that Al Mualim was the final target, the Apple of Eden's map and Desmond's realisation that the Templars are alive today. The game does not resolve the larger story: it opens it.
What it means
The game is about trust and control. Altaïr learns that his master used the Creed to control him, and Desmond learns that his captors have the same ambition.
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Where this comes from
Every sentence above is built from facts confirmed by at least two independent sources. Sources used: Wikipedia, Assassin's Creed Wiki.