I really don't think that Reiji's mom is going to kill Gen, it would not make any sense. She still hasn't got the money and complying with the requirements after killing the towns boss son would be too difficult and inconvenient. What this show is that the chain of backdoor relationships goes deeper than we thought. I also don't think that they are going to do the nasty. They seem to have more animosity between each other than any sort of sexual relationship. If they had such a relationship then Gen wouldn't be that annoyed and reluctant to meet or even enter the room with here. I think that It makes more sense for this to go along with what I think is the central theme of the story "leaving without control over your life". As I have pointed out in other comments, all of the persons who interact with Reiji (except for Nagi and the author of the novel) share as a trait the fact that they, at least feel like, they don't have any real control over their life. So they try to proxy that control by exerting control over Reiji's life. The sensei is the most upfront about this and that is why she has the most agency on driving the plot so far, the chubby girl wanted to be "Reiji's savior" and have him go study with here. So now going back to the mother and Gen; from the beginning we witnessed the mother coercing Reiji into "supporting" the family as soon as he finished school, and the Gen has stated that he plans to have him work by his side for the rest of his life. Gen has also revealed the extent on which he plans to have total control over Reijis future talking about how he would even find him a "good wife" and shit. That leads me to believe that leads me to believe that the mom and Gen have been colluding al along to tailor Reijis life and prevent him from ever living them; as well as constantly monitoring him, on the one hand the mother keeps him in check at home and Gen on his after school activities. Now consider this what does the mother thinks that sensei does understand? I think she referees as to how the sensei does understand what kind of person Reiji is, and that is the type of person who would put other peoples needs over his own self, who thinks he has to shoulder the responsibility over the lives of everyone who is important to him and who would only be happy if he thinks he has successfully lifted that weight. That is why after finding the thruth about his mother he asked sensei for a loan and then promised to save chakko and his whole family. Now my theory is that this same trate of his that drives him into try to take responsibility for everything resulted in some sort of incident back when he was little. At that point both the mother and Gen probably realized that the only way for him not to drift away trying to shoulder everyone's problem. So the only way to keep him from doing that is to coerce him into staying, the mother does so by constantly guilt tripping him into believing that he has to bear all the responsibility for the life of here family and Gen conditions him into developing total submission to him. We know realized that in the case of the mother this is not true as soon as she realized that Reiji is sleeping out of here grasp she immediately states that she has no problem with throwing the whole family away as long as she can stay with Reiji. In the same way when Gen feel this too he immediately resorts into guilt tripping him into thinking that he owes his family and Gen his life. So my final theory is that it was Gen plan to have the mother fuck Gen's father as a way to grantee a working place for Reiji in this town and further locking him in. And that whole story about here doing it for years is probably somewhat fake and just Gen trying to lock Reji. But now they both need to re-asses their plans.
@Gladiator02
The Story of the Lady Who Wants to Nurture a High School Boy
Bruh.. that is just so on point hahahah