We have time travel. We have a dead physicist who killed himself. Fuu seems to think the time travel properties can be solved by her father's contemporaries. We know that Yotsuha's mom turned on her extremely suddenly after the suicide of a particular person. While we don't get direct confirmation the suicides are related, it feels like it could be going that way. We know the brother explicitly tells her not to kill anyone.
We still don't know who Yotsuha's father is. We still don't know if the mom's car accident was really an accident. We still don't know why Rei accuses Yotsuha of being a murderer. We still don't get why he betrayed Uichi to bullies, or what the deal with the strange insult was. We still don't know what Uichi meant when he said it figured that Yotsuha doesn't remember Rei's name, or why he didn't tell Yotsuha something when pressed.
I want to keep in mind that no twist has come out of total left field in this story yet, far as I can tell. There's always a setup somewhere, though sometimes it goes really far back, and the connections aren't always clear. But so far we really haven't been shown enough to peg someone as the mastermind, because we haven't been able to solve the unfinished mysteries this chapter calls out so blatantly.
I think Mom did something to Fuu's dad to get him to kill himself. For lack of a better way of saying it, I think the idea he did it because he was over worked is false. I'm not saying it doesn't happen, but it doesn't right here.
I still think Fuu is innocent, I think Clover is someone else. Fuu-chan basically holds Yotsuha's heart in her hand and could really mess her up if she felt like it. I don't think she'd need someone like Rei to do her ill-will.