This is less of a prediction and more of just a writing exercise for me since I'm bored. 

So let's get to it. The branching path will be Hajime awakening his memories but having both of his personalities still existing leading him to basically be caught in this weird DID situation where he's constantly fighting himself and has a new hatred for the other students.

Ch.1 plays out a little differently with Hajime's sudden shift they call off the dinner party which leads Nagito to adjust his murder plan, he considers targeting Hajime but becomes motivated to kill peko when he learns of her relationship with fuyuhiko with his goal being to create ultimate hope within fuyuhiko. Fuyuhiko learns about this and kills Nagito first, hides this from Peko with the intention of dragging out the trial just do Peko can see who to watch out for. He would plan to confess in the end not wanting to get Peko killed and orders Peko to kill and survive.

Ch.2 Has extremely heightened tensions. Mahiru gets on her bullshit and starts lecturing Peko about grief causing peko to fucking lose it and decide to kill mahiru and hiyoko. She lures them to a spot and attacks them, injuring hiyoko and Mahiru but before  Peko can finish the job the body discovery announcement plays causing her to pause since if she kills them she wont be able to escape. This hesitation allows mahiru and Hiyoko to gtfo before Peko can restrain them to kill them later. They run into Akane and Nekomaru who went looking for them and peko is forced to back down. Chiaki is dead, Hajime is freaking the fuck out due to his memories and refusing to let anyone near the body, peko shows up and everyone learns what happened, mikan starts taking care of hiyoko, and monokuma makes a rule that forced Hajime to let them investigate. Soda killed chiaki because he won a contest,learned there was an imposter and saw a photo of the real chiaki's corpse. He confronts her but when she cant tell him anything he panics and attacks her. 

In ch.3 Hiyoko stops bullying Mikan as thanks for healing her wounds which makes Mikan think that Hiyoko doesnt care about her and she starts antagonizing everyone to try and get attention. Teruteru is having a character arc by the way and is learning to not be as creepy. Twogami has completely lost control of the group and Peko is on her line wolf type beat. Gundham is a repeat killer and targets Akane. Nekomaru tries to survive her but they both die in the process. Motive uh 4 dark devas are threatened, or despair disease or, idk i would think more on this one. 

Mahiru tries a different approach and accepts that overcoming despair is not as easy as she believed it to be. Her peko, and hiyoko have a heart to heart and peko cries and abandons her revenge quest with them all swearing to escape together. Mikan and hiyoko also make up and everyone in the group resolves to change, except for hajime. Ch.4 motive is Hajime telling everyone that theyre in a simulation and that Junko is the mastermind. He doesnt reveal anymore but says lies and tells everyone that they are all in a competition and in the real world the winner gets whatever they want. Ibuki kills sonia to achieve her dream of getting band mates.

In ch.5 Hajime loses his internal battle to izuru who decides that this experiment has failed, he plans to escape, kill every ai junko, and then himself. He targets Mikan because his main plan is to bring everyone to despair to stop them from investigating properly. Hiyoko is rendered unconscious by izuru who also tries to frame her and then he fully unloads and reveals tha full truth of everyone being remnants, what junko's plan was, who the real chiaki was, what happened to natsumi, sato, teruteru's mom, and even tells twogami about mitarai and lies that twogami killed him. Everyone is plunged into despair but Mitarai joins the simulation and uses administrator privileges to force Ai junko to assume her real form as she runs the 5th trial. Izuru dies happily saying that he couldn't have predicted any of this and praises junko. 

Things may know be a bit weird with Junko openly trying to bring them into despair and convince them to escape with her. Tempting them that they can bring all of their friends back and she'll just take Mitarai's body since he's here. Mitarai ends up killing Junko to erase her and despair. The group still decides to hold a class trial as they now know there is no way to bring everyone back since kamakura is dead and no one has the talent to bring the others out of their comas. In the end even though they are.tempted to stay in the simulation forever with Ai versions of their friends they all decide to leave and face punishment for their crimes. 

This would definitely need work and cleaning up a bunch but hey it was just an exercise 

How I would write 2x2