I can why it's confusing for some readers, but I think it really helps to take the time to reread certain parts of the story. I'll try my best to explain for any readers who are confused.
WARNING, SPOILERS:
This story features characters who have mental illnesses of varying degrees.
Hirasaka Koushirou: He was a hikikomori (someone who is a shut-in their own room/house). I believe this is due to his feeling of inability to protect his childhood friend, Yuuto. With no one to believe that Yuuto was kidnapped and coincidentally seeing the "kidnapper" at a hospital, he thought he had become crazy. Due to the stress, he became a hikikomori. He overcomes this illness though, because he is determined to find Yuuto, who he believes really existed. Then he meets Okitsu Ryou, who tells him he knows Yuuto. Okitsu tells him to attend a certain university, and that's where Hirasaka finds Yuuto. Hirasaka was probably confused at first, because Yuuto took on Okitsu Ryou's identity to attend school (hence why Hirasaka told Minami, "The one I was looking for was a different person.") His suspicions that "Okitsu Ryou" is really Yuuto are confirmed by seeing Yuuto's reaction to his story of his "unseeable friend" who had been kidnapped.
(Okitsu) Yuuto: He has amnesia. Due to experiencing trauma as a child, his grandpa (the man Hirasaka thought had kidnapped him) took him away to take care of him. He then performed an "experiment" (hypnosis?) to erase 6 months worth of Yuuto's memories, as he believed it was better for him. This is because Yuuto had been constantly dragged around by his mentally ill father until his dad dies in Hirasaka's town. He told Hirasaka his father is ill and believed his father was always "sleeping," when his father had been dead the entire time. Due to fear of his father finding him (as he wasn't told his father already died), he ends up taking on Okitsu's identity to attend school. Hirasaka finds him, but realizes Yuuto does not recognize him. Hirasaka doesn't force him to remember, but brings up the story of his "unseeable friend" as a way to get Yuuto to remember him. Yuuto took a while to recognize Hirasaka, due to Minami telling him that Hirasaka's first name is Koutaro, not Koushirou. Yuuto only remembers Hirasaka due to a notebook which the real Okitsu Ryou had written in his memories for him. Due to Hirasaka's story, Yuuto also finds out that his father had died in the house. He had no idea, as Ryou and his grandfather had hidden it away from him. This is why he abruptly leaves the table. In the end, Yuuto decides to fully regain his memories and takes on his own identity again.
Okitsu Ryou: He has claustrophobia. He already had it when he met Yuuto, and it's said that it is due to how he was stuck in an elevator as a child. Ryou is not related to Yuuto, but treats him as a younger brother. He was a patient of Yuuto's grandfather. He protested against the removal of Yuuto's memories, and insisted that he would write them down in a notebook for him. Since he can't really attend school due to his claustrophobia, he lets Yuuto attend school with his identity. His claustrophobia gets better when he's with Ibu, as he couldn't stand staying in classrooms, but he willingly went down into Ibu's narrow library TWO times. Once was to speak to Ibu, and another was to chase the old man who was stealing Ibu's work. In the extra, he also preferred staying with Ibu in the house, rather than going outside to play with Yuuto, Hirasaka, and Minami.
Ibu: He has paranoia (?). Though it may seem that he can "read" people's minds, it's mainly due to his strong perception and deduction. He believed that he was not the writer of his own stories, but someone who was writing for them. This ended up being part of his paranoia, as he was being heavily influenced by the old man, who insisted that Ibu's ghost-writing was his own writing and that Ibu was writing it from his "mind." So Ibu started thinking that his writing was not his own, but something taken from other people's minds/experiences. The guilt made his paranoia worse.
I think this story really deserves a few re-reads, mainly because past details will make more sense after knowing the entire story.
Yeah.. that was one part that actually confused me. I think Yuuto has no idea about it because he either didn't tell Okitsu, or Okitsu secretly decided not to write it down in the book. I don't know why he choose to "blow" Koushirou. Like, does that mean he had been sexually abused by his father without knowing (because how else would he know how to give a blowjob)? But there is no further of such sexual abuse, despite it being something that could possibly change the whole tone of Yuuto's story into a much, much darker one. Too bad the author didn't go into more detail about that, since she just left it as a single comment from Koushirou...
well me too have thought that Yuuto was sexually abused by his father and his father died probably because he killed himself after.That's why the grandfather decided to erase the memory of Yuuto, indeed his grandfather was a hypnotherapist...what have me confused is this part http://www.mangago.zone/read-manga/wandervogel/hs/hs_chapter-2/24/ because what Shiro say, don't match with what the grandfather said here http://www.mangago.zone/read-manga/wandervogel/hs/hs_chapter-2/23/ and the theory about sexual abuse is very confusing ,like it seems that but don't….i don't know anymore when i think i've undertood the story , i don't and i'm even more confuse ┗( T﹏T )┛ sorry if i've made some mistake ,but i don't speak well.if so please correct me so i can improve (●'◡'●)ノ
3 things make me think there was suggestion of sexual assault before the father died...
1, the fact that he 'looked like a girl'. Boys aren't generally mistaken for girls, even when they have longish unkempt hair, meaning he had possibly been dressed and groomed to look like a girl.
2, the grandfather's comment that his father was obsessed with him after the mother died.
3, the oral sex thing.
i almost cried when he said that