In the very beginning of the game the apple is stuck in the staff (from AC2's battle with the pope) which is stuck in the ground.  When Ezio tries to pull it up it recedes into the ground along with the apple.  So where did the apple in this game come from?  One minute it was sealed underneath the floor in the vatican, and the next Ezio and Mario had it on top of a building in Rome.  The game never really explained this. 

If you notice when the papal stuff recedes into the ground the apple is no longer on the top. Ezio had pocketed it, he's sneaky.

Ezio is really Eve, at the end he eats the apple.

it came from eden

God's butthole

I seem to recall Ezio yanking it off the staff before entering the vault. I also recall Ezio saying that Papal Staff was also a piece of eden....but I might be wrong on that.

" I seem to recall Ezio yanking it off the staff before entering the vault. I also recall Ezio saying that Papal Staff was also a piece of eden....but I might be wrong on that. "

the garden of eden probally.