Well, here's a quick review of the 1st one, as Altair, you are betrayed by your master of assasin's (the boss) he want's the apple of eden. because it has special powers. He get's it, and than you'll fight with him, ofcourse you win, and you get the apple. But the people of the city think you killed the "boss" for no reason...
So Altair puts the apple in a secret place.
For Desmond Miles: Well he needs to find out why he's beeing hold, and wat his relationship with Altair is.
He founds out that Abstergo are not the good people... They are the templars of the present day