I think Fate might actually be crying for how Nanoha has signed her own death warrant... if Mami back there isn't enough, look at all them gears reality-marble Unlimited Blade Works style off to the side.
Considering what we don't see, where Fate's eyes are, and the nature of a "Wish" that Nanoha might have made...I think Fate might be crying for a different reason, If You Know What I Mean.
