At the end of Brotherhood Lucy (revealed to be a traitor) is stabbed and killed (presumably) by Desmond after his hand is forced by the apple (being controlled by juno, an ancient) they find in a long hidden ancient vault, the location of which could only be discovered by reliving more Ezio memories.
Desmond slips into a coma.
Credits.
In Revelations, it's revealed (see what I did there) that Desmond was placed in an animus by his father, (an assassin too) to prevent him from becoming a vegetable (obviously sound medical advice there.) While inside the animus he meets subject 16 (a descendant of Ezio.)
Oh and there are a few Altair memories that lead Ezio (yes Ezio relives Altair memories while Desmond is reliving Ezio memories) to Altair's vault which is where he put his own personal apple. Ezio decides enough is enough and leaves the apple where it is.
The world is still going to be blown up by the sun and it is revealed in a pre-rendered FMV cutscene that thousands of years ago there was a super advanced civilisation of humans living among skyscrapers and shit until the sun fucked them up. The parting shot of this FMV is a close-up of a mother clutching a baby presumably an ancient ancestor of Desmonds.
Before the end of the game desmond is approached inside the animus by jupiter (one of the ancients) and is told that they developed lots of techniques to prevent severe solar death from happening but failed and that all knowledge of their attempts is stored in a vault. He tells Desmond where the vault is.
Desmond wakes up and proclaims "I know what I have to do." Somehow the team of assassins have managed to bring him to this vault already, they go inside, it powers up and credits roll.
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