And if history repeats itself, for myriad potential reasons, in another decade or so, a lot of innocent people are going to die at this boy's hands. Madness, terror and suffering is only a matter of time; Zack's talking to a dead man before he even has the chance to grow into a man at all. Fate isn't particularly kind to any of them.

Were is past tense. "But not anymore."

And Zack is very much alive, which had implications, so he bends what little knowledge he has about friendship to working the puzzle out. It was obvious Zack was defensive of the decision to not kill Genesis, be it by orders or as mercy, and he didn't talk like they'd become enemies.

Were. Something got removed from the equation, and it wasn't Zack. How do you become not-a-friend, without losing that friendship in the doing? "When do I die?"