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Well as you know then Templars have found Desmond and tried to use him to access his bloodline - Altair and see what he did with the apple of Eden that he had obtained - which you will also find out what he actually did with it in Revelations. They've also discovered that there is more than one Apple and where they are located in different parts of the world - then the breakout etc and Desmond escapes with Lucy and they submerge into animus this time as Ezio who is like Altair's great grandson or something - he'll actually obtain another Apple as you'll find out when playing.

Basically the Apples are very powerful artifacts created by a race that has existed millions of years before humans did - they were humans too but much more advanced and created these powerful artifacts that we just started discovering now. There is a twist in both #2 and the Brotherhood. Revelations twist was so-so but the bits with Altair were very nice additions indeed as I always liked him more as a protagonist than Ezio. Apples allow control of individuals, the wielder can basically subdue people within it's active range and make them do what he wants to do, or just kill them outright by destroying their mind or something - must be pretty painful.

Disconnect and self destruct, one bullet a time.