What? School Days had a manga too? I guess they did the bad end too, huh?
Anyways, what seems to have happened is that Kotonoha tried to kill off Sekai, and Makoto was sent to the hospital because he got in the way. Before Sekai came to visit, she went and killed Kotonoha, and at the end, Makoto realizes it's all his fault all this happened (which it is). you mean like that?