Subject 16 discovers this recording while hacking into the Abstergo mainframe.
Warren: Lucy, this is where your background comes into play. If our experiments with Desmond in the Animus aren't going well, you will remove him from Abstergo. Take him somewhere he will feel comfortable divulging his secrets. Your Assassins should do the trick. Since Desmond will be reading our emails, we will ensure that secret communications between you and the Assassins go through unimpeded. Once you are imbedded, I will come to pick up the Animus tapes. Make sure you look very upset. You need to be convincing. Desmond will lead you to the Apple and then you bring it right to us. We're counting on you, Lucy. You have served the Templar Order well, and we never forget loyalty. Oh, yes. Once inside their hideout, perhaps you might ask the Assassins why they left you alone for so many years.
He then gets this email from Lucy:
07/2012
Clay,
I've seen the security records from last night. You must want an explanation. I had hoped to tell you about it little by little, to get you on my side, but it's too late now.
William is using us. In this war. In this war against the Templars, he doesn't think about the lives he's hurting. We aren't people to him. How can we trust someone like that? Clay, you of all people should understand.
Abstergo cares about helping people. They understand the realities of the world, its limitations.
But I know that nothing I can say now will really change your mind.
I've deleted the security records. Vidic will never discover the breach. I promised to protect you, but I can't let you leave. William and the others must never know.
I'm sorry.
-Lucy