Not what I was expecting, but surprisingly not surprised, given that this is a manga. If they don't show the "antagonist", there's a 150% change that it's a character you know. And there's always a 43% chance of time travel paradoxes, alien invasions, or "it all being a dream" randomly appearing.
Still feels a bit ... meh though. Hopefully it'll at least do some more with the end, and not just a "oh yeah, they reconcile and become one and live on happily after talking for a few panels".