Alright, I have a theory, I'm gonna try calling it. Backstory of the island is at least somewhat accurate. There was a monster, it fell in love with one of the offering girls, and stopped attacking the island.
Kon resembles that offering girl, and the Kaijuu is in love with her. It saved both Kon and Furuka when they fell in the ocean and took a swipe at Mari because she was bullying them, but also when Kon and Furuka started doin' it, it got jealous and separated them.
Now it's starting to venture into Yandere territory, booting Furuka off the cave/cliff, but Kon followed her so it had to pull it's punches maybe? I dunno, my theory gets a lot fuzzier as we get into this issue.