At the start of the game the Player can be killed by Yukari if they refuse to help her, since she already told them her plans. This is a non-standard joke ending, and the only time the Player is referenced in game.
Deciding he can't be witness to her crimes, Yukari reveals her plans and kills him when he runs to call the police. In the true route of the game, while injured he will reappear and reveal what he found out, going to attack her. If Yukari didn't kill Miho earlier she will arrive to defend Yukari and kill him.
Miho requests Yukari deal with him since he stalks her. If she believes what Miho told her, she will kill him without hesitation.
Killed by Yukari in the True Route of the game after she locates him and rids of Tanaka a final time.
In two routes Miho will be killed, one of which sets the game up for a Bad Ending if Yukari decides Miho can't be trusted and rids of her early in the game.
In the other, Yukari accidentally gets her killed by sparing Wakabayashi- who implies he would be enacting a murder-suicide with Miho.
Only in the true ending is he killed alongside everyone else.
Tanaka has several deaths that can be triggered throughout the game. In one he is taken hostage by Akira and can be killed by Yukari, or if she spares him they flee to another Classroom, only for Akira to corner them and kill them both. In another route not involving Yukari, Tohru gets angry and kidnaps him, revealing his feelings for him and his plan to cut his legs off to make sure he can't escape.
One one of the Main Ending routes, if the Player messes up he will be killed alongside Yukari and Miho if they fail to defend her from Minami. In the True Ending it was revealed that Yukari killed him.
After she strikes to attack Yukari, Miho will defend her and Yukari takes advantage of this to kill her sister, apologizing for what its come to. In the True Route, Miho will be the one to kill her instead.
It is implied she is injured or killed when Tohru confronts her and Tanaka. In the True Route of the game, it is revealed that Yukari killed her, along with Tohru after Miho attempted to protect her from her sister.
In the Final section of the game, he can be killed alongside Miho and Tanaka if Yukari fails to avoid her sisters attack. It is also implied he was one of those murdered with the others in the true ending of the game as well.