In the original story, what he says is not clear. I think he said, "honto ni ai shiteita" (I really did love you) before he shoots and kills her. It's about the same amount of mouth flaps for the animation.
The movie goes silent as he talks, so you never actually hear what he says.
Based on context, you can guess that he's either saying "I really did love you" or "It's not creepy at all that the naked albino child behind me is a clone of my wife."
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