GAME 1:

Junko Enoshima doesn’t exist. She’s just a made up person. Mukuro doesn’t have a sister. Junko was just thought up by the mastermind.

Using this fake ‘person’, Byakuya corrupted Mukuro with despair, bringing her to his side, and caused the WMDIEITHOM (Like hell am I typing that all out). He started the mutual killing, make Mukuro dress up as ‘Junko’, and, following canon, murders her for the sake of despair.

This continues on, in canon, until the trial. Everyone is convinced that ‘Junko’ is the mastermind, vote for her, and get it wrong. Togami smirks, walks up to where Monokuma is, and announces that there was no Junko, Junko doesn’t exist! He smirks, tells everyone that they’re nothing but idiots, and reveals himself as the real Mastermind.

The he executes everyone, because they all got it wrong.

GAME 2:

Since all of class 78 are dead, the one who does the rehabilation program is Chiaki Nanami. She’s from another place, and, with determination, captures all of class 77, and does the program.

Continue on as canon, until chapter 5. Instead of Nagito successfully making Chiaki the killer, he kills himself instead. Chiaki reveals herself as the traitor, and nobody dies.

In the final trial, Togami shows up unsuspectingly, reveals himself as the mastermind, and goes on to tell them how he murdered his entire class, etc... The he provides a choice: Shutdown and kill him, but retain memories of Ultimate Despair, or Graduate, and retain their memories, but he would take over the dead students bodies. Unlike the first game, this ends happier, as it follows the same as canon, and, as the game shuts down, Chiaki smiles, telling Hajime she will see him again in the real world soon.

DR:AE

Two changes: Firstly, Komaru has no partner. Instead, she has Izuru. This follows the same premise, until Izuru reveals himself as despair. Komaru and him fight, and, in the end, Komaru gets away, and saves herself. The rest of the game is the same, just she does the whole thing alone, Without Toko.