I think Desmond will go to Masyaf to get the other apple, the hook blade, the other hidden blade, Altair's hidden blades, and Ezio's sword. Desmond would wind up with 5 hidden blades, 2 hidden guns, a sword, and 2 apples. It would be good for the assassins to have another apple.
And I don't mean that Desmond will wear 5 hidden blades, that would be a funny sight.
Never mind, Altair's apple is gone, so Desmond wouldn't have it.