The final scene of the anime - the balloon rising up from the depths all the way to the surface, passing by all the challenges Riko and Reg managed to pass...it was a beautiful scene. Especially with the music on top of it. That track has to be one of my favorites from the OST.

Also Nanachi's flashback was heartwrenching and painful to watch in the best way. While I don't think Mitty's transformation was handled quite as well as Riko's arm breaking, it was still a viscerally unpleasant scene. So that was nailed down pat. The scenes after it, though, made it even worse. Mitty crawling out with her half-destroyed body was hideously grotesque, far worse than in the manga...so, uh, good job guys. I didn't know you could make that scene more unpleasant to look at but you did.