Ah! Well, somehow causing a war would certainly destroy their innocence, and there are almost innumerable ways to start a war. Genocide would also ruin their innocence, but I feel like it’s less plausible. It would work best if whoever your antagonist is no longer had their innocence. Either their from our world (like in Out of the Silent Planet By C.S. Lewis) or they’ve already had their innocence destroyed.
Another thought would be a certain command that would cause lots of innocence loss if violated. (like the Fall of our own world. Also like the near-fall of C.S. Lewis’s Paralandra). This command could be almost anything, but the regardless, the bad guys must have a convincing reason to break it.
Hope that helps!
Quoth the raven, "Nevermore!"