User blog comment:Aegis Runestone/Does anyone else dislike Lucy being... *spoilers*/@comment-5007412-20120415182100

It does make sense when you think about it. Lucy didn't escape with Desmond because the higher ranking Templars knew about the plan, Lucy would use Desmond, Shaun, and Rebbecca to get the apple, then when they got it Lucy would have the perfect opportunity to kill William Miles (the current Mentor of the Assassins) thus destroying the Order in the proccess.