Editing Desmond Miles (section)

===Obtaining the Apple===

:'''Harlan''': "''Shit! He's gone into shock!''"
:'''William''': "''Put him back in the machine, it's the only way to fix this''"
:'''Harlan''': "''But the Animus did this to him!''"
:'''William''': "''Am I the expert or not? Do it!''"
: —William Miles and Harlan T. Cunningham, regarding Desmond's health, October 2012.<sup>[src]</sup>

After finishing in the Animus, Desmond and the others learned that the Apple of Eden which Ezio possessed was hidden under the Colosseum. Upon traveling to Rome, the group separated, with Desmond climbing through the ruins of the Colosseum as the others tracked his route above ground. While he headed deeper, Desmond saw several visions of Juno along the way, until he eventually arrived at the Basilica di Santa Maria in Ara Coeli, where he unbarred the door cover for the other Assassins to enter the building.

Upon synchronizing his DNA with a strange pedestal, several levers and structures lowered from the church's ceiling, to which a brief vision of Ezio showed Desmond the way to climb up. Along the way, more visions of Juno appeared, and she explained that the Vaults were made as the only proper places to hide away knowledge. Eventually, Desmond reached a structure with a lever, where he saw a vision of Ezio lowering it. Copying the phantom, Desmond also lowered the lever, which caused another pedestal to rise from the ground, along with a set of poles that Desmond used to make his way down.

Once again synchronizing his DNA with the pedestal, Desmond activated an elevator that took all of the Assassins down to the chamber below, which held the Apple in its center. As it was noted that a free-running course was the key to bridging the gap, Desmond maneuvered his way around the chamber and lowered several lever throughout the course, all the while seeing visions of Juno scattered throughout. Finally, the stairway leading up to the Apple was raised, and the Assassins noticed several symbols being projected around the room as they walked up towards the Piece of Eden.

However, as Desmond took the Apple of Eden from its pedestal, Juno's voice was heard, saying that Desmond's DNA had activated the Apple. Juno then took control of Desmond's body through the Apple, and forced him to stab Lucy in the abdomen with his Hidden Blade.

After collapsing in the Colosseum Vault, Desmond was taken away by the Assassins. Having slipped into shock at the ordeal, his unconscious body was recovered and transported to an unknown location.

During this time, Desmond was placed back into an Animus by William Miles and Harlan Cunningham. In this session, Ezio and Leonardo da Vinci were shown to have discovered a smaller Vault in Rome, and as Ezio's DNA had activated the Vault, a set of coordinates that was intended for Desmond were projected, showing: 43 39 19 N 75 27 42 W. Finally, after reliving more memories, Desmond's condition worsened to the point that he entered into a comatose state.