Kimi's true identity is a 22 000-year old God (basically a creator of deities like Cthulu). She trapped the town in a time loop for 20 years to repeat the year 2000 because she was interested in humanity to see if they deserved Eternity.
Enter Yuri's family, a cult trying to resurrect a god (a weak minor deity Kimi created) through human sacrifice and trying to kill everyone in the complex.
Kimi was killing off anyone close to the truth by turning them into moss so they wouldn't be sad.. not to mention people that did find out basically wanted to die or go crazy before being turned.
Then Yuri's family broke their facade, which in turn made Kimi "bored" drop her persona and decide humans are shit, killing Yuri's family Brutally as punishment, he broke the time-loop and left, deciding humans don't deserve eternity.
Khan got to live because he'd followed Kimi's instructions, which saved him when Kimi broke the time loop, which then was the only one left alive in the area before the time-loop was broken.
Much of the lore surrounding Kimi leaves a lot of questions that are never answered. She also implies that Koshide’s ritual sacrifices brought forth something other than what they intended but didn’t elaborate.
It was far from as pretty as Fena but had some excellent music and considering it was the writers first anime and the studios first series, it was an admirable effort. For all its flaws I do think it was a solid suspense thriller that we’ll be able to find more details in through additional viewings. It also probably benefits from being watched all at once.