The modern-day Assassins, including Desmond Miles, make their escape and go into hiding from the Templars. They take refuge into modern-day Monteriggioni, which has been preserved as an historical site. There, they setup the Animus for Desmond to explore deeper into Ezio's past and discover more about the missing Pieces of Eden. Ezio's story takes place immediately after the end of AC 2, and has him leaving Rome to head back to Monteriggioni. There, he is ambushed and the Piece of Eden he has found is stolen. He must head back to Rome, which has since been seized by the Borgia, rescue its people, and recover what has been lost.
You take on the role of Ezio as he use his assassin skills to free Rome and fight against the Templars.