Board Thread:Series general discussion/@comment-18014300-20170103020539/@comment-26160856-20170120225925

Here's how i would explain them:

I.  Same, Ezio thought he wasn't a Templar. "You dare to lecture me? I am the hammer of heretics, the light of España, the honor of my order"  with "order" he most likely refers to the Church, but still it is open to interpretation.

II. Because he is secretly an ally, the Templars would think that the Assassins have the Apple, but it is easier to give it to someone else to hide it. And it always worked until the Animus was created.

III. It is implied that the Assassins and the King are allies. It happened with the Egyptian Brotherhood as well. They gave a dynasty a Piece of Eden to help them overthrow a Templar goverment/dynasty. And why would Ezio take an Apple that is been guarded by an Assassin ally?

What i want to know is what the hell happened to Apples #1, #3 and #5. They were supposed to in Templar hands the previous century.