Okay brief summary time.. Obvious spoilers for all the games. I'm focusing on the Desmund story not Altiar or Ezio.
In assassins creed 1, Desmund Miles and normal guys gets captured by templars who explore his genetic memories using a device called the animus. They want to find the location of the pieces of Eden (devices left behind by the race before humans which have incredible powers, in fact most of the bible is based on illusions created by these objects0 which they will use to rule the world (which they see as a good thing as it removes conflict and disunity). He enters the mind of his ancestor Altair, part of a secretive brotherhood of assassins, in the holy lands during the time of the crusades. He tracks down and kills Templars who are in positions of power. At the end of the first game the Templars use Altiars memories to find the locations of the pieces of Eden and
In assassins creed 2 Desmund with the help of Lucy who was apparently a templar in the first game but is actually and assassin spy, escapes the Templar hideout and goes back into the animus and in order to train to be an assassin himself. He enters the mind of an ancestor in renaissance Italy, Ezio and follows his memories as he takes revenge on the Templars who murdered his family. At the end he finds out some sort of global catastrophe that wiped out the forerunner civilization is returning in 2012 (relating to the Dayan calender end of the world thing) and that he must stop it using the pieces of Eden and other technology left in hidden tombs like places around the world. At the end the templars the warehouse he has been using to train in and he and the other assassins manage to flee
In assassins creed brotherhood you return to Ezios villa in modern times to locate the apple of eden. You explore Ezios memories after he becomes a master assassin as he eliminates the Bougia in Italy. In the end you find the apple in present time but a strange image of a forerunner speaking of prophecy makes you stab Lucy and fall into a coma.
In revelations you are plugged into the animus in order to keep you mind from unraveling and you continue to explore Ezios memories. Exzois now an old man in Constantinople finding special keys left behind by Altiar to enter his secret chambers. You fight the usual Templars and Byzantines to recover the keys. In the end both the stories of Altair and Ezio are wrapped up nicely and you are shown and nice image of the apocalypse. You awaken knowing what to do to prevent the end of the world.
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