It definitely gets confusing. I didn’t enjoy the game at first, and I think experiences can vary widely depending on a player’s chapter selection. I ended up with a stretch of all school life stuff early on, with more of the school crushes and inconsequential dialogue than the more interesting sci-fi bits (I hated Megumi’s chapters). Putting off Natsuno’s was also a mistake, as she ended up being my favorite character. The game has grown on me since.

The stuff with Chihiro gets a little wild, but it essentially all boils down to

spoiler

a difference of opinion in how to get out of the mess, and the access to do so. Chihiro wanted to blow it all up again, and she needed to put herself into Iori to loop again with herself intact. It being the last loop is simply a resource problem. The simulation had been running through many loops for an untold number of years (likely many millennia). The idea of another loop being possible only by scaling it down (and presumably killing some of them) was a big part of why the others wanted to make their stand at that time.