Yotsuya, our titular heroine actually dies, replaced completely by Kukuri our resident crossdresser ghost as a result of Sensei actually following through on murdering her ghost while she was swapped for Kukuri, basically the thing he's been wanting to do since the very beginning of the series, and showed signs of interest in till the very end, but everyone is always like "lol it's fine to have this clear psychopath around he's not going to do anything. I know he almost completely buried Keita in a hole one night he thought our boy was a little too close to Kukuri but we'll play it off as silly". Long story short, Kukuri decides (s)he's going to kill sensei after this happens, but Keita stops them with a "don't let them run away by dying" speech. Keita almost kills Kukuri in Yotsuya's body but can't bring himself to do it. Sensei subsequently gets turned in regarding a murder Kukuri actually convinced him to do as revenge for them killing her in the past (cause surprise surprise Kukuri actually had a dark side too, and that's actually what makes sensei so messed up). A small time skip later, Keita is falling apart. Keita's other female friend (whose name I can't remember) tries to cheer him up, using a "aren't I good enough move?" which fails, but he makes her think he's feeling okay now. Cut to our protagonist standing on the roof of the building that has been the focal point for this entire series, and attempts to kill themselves by jumping so he can reunite with Yotsuya, but is stopped by Kukuri. He has a huge melt down, clings to her, calling out to Yotsuya as though it's really her, and screams out how it just can't be true that she died. Kukuri replies they'll be together forever.
Time skips four years. Kukuri is casually meeting with sensei who is out and about already. Sensei asks if Kukuri and Keita actually got together and Kukuri agrees. They've kinda had this messed up relationship where Keita knows Yotsuya's gone but is kinda just going with the flow. Kukuri gets a notification and then says she's going to head for a date with Keita and we jump to sullen Keita still obviously carrying a lot of baggage, until he sees a little girl running by and tripping. He seems to recognize her on some level (as Yotsuya), suggesting it might just be his imagination, but he then asks her if she's happy, she says yes cause of course she says yes she's a 4 year old girl, and then he starts crying. She puts a bunny bandage on him as some kind of cute "pain go away" thing (it should be noted that bunnies and Yotsuya are kinda connected). Keita has now convinced himself this random girl is Yotsuya's reincarnation (she probably is) but it's clear a weight has been lifted from his shoulders.
He meets up with Kukuri, and mentions a wedding dress he gave her to wear back in chapter ~31 during a "confession" he received (for reasons) and rejected from Kukuri, and suggests they actually go through with it and get married. Kukuri is stunned and asks if they're really okay with them, specifically using [boku] when asking instead of the [watashi] they transitioned to when they took over Yotsuya's life, and Keita agrees. He says that even now, he can't forgive Kukuri for what happened, but her second chance (at life) is going rather well (referring to Yotsuya)
It ends with a phrase that's been used a few times always slightly different throughout the story. "I have a girl I like, up until now, and from now on as well, forever." with a picture high-school age him and Yotsuya smiling together.