User blog comment:Aegis Runestone/Does anyone else dislike Lucy being... *spoilers*/@comment-3981209-20120416203412/@comment-1888015-20120416223807

Perhaps she's sad because while she didn't want Clay to leave so that her secret got out, she didn't believe he'd go to the extreme of having a mental breakdown and commiting suicide.

She could have genuinely blamed herself for his death.

Personally, even though I know what's supposed to be her true alliegance, it could be said that after feeling abandoned for so long and then coming back to see Rebecca and Shaun, she sort of regained some hope in the Assassins, even though she had her reservations about William Miles.

The Lost Archive makes her out to be heartless, but what's stopping her from just being conflicted with who she's supposed to support?

For all we know, she could have wanted the goal of the Assassins, to have the free will to make mistakes and learn from them; but she might have sided with the Templars because even though their satellite idea was enslavement, it still didn't cause the death of people, which the Assassins don't feel too bad about doing if it helps humanity overall.

If that's really what happened with her, it kind of makes her death an unfortunate, but necessary tragedy.