Komaru Naegi and Toko Fukawa(from the first game) attempt to save the world from dangerous Monokuma's. The events of this game take place during the second and first game. Komaru Naegi has been trapped inside an apartment with no connection to the outside world for 1/2 years. Every day she goes to the door leading out but it seems to be locked from outside. However, on this one day food was delivered to her and she bang on the door to let her out and to help her but sharp claws almost strike her face. A huge Monokuma breaks open the door and begins to chase her around the apartment. After she gets out of the apartment, she must run to the elevator which to her surprise brings out Byakuya Togami. He gives her a hacking gun(that is designed as a megaphone but shoots bits of codes at anything and makes it malfunction and break.) and tells her to run to a nearby restaurant and find a member of Future Foundation. Monokuma's enter the restaurant and start attacking the customers. Afterwards, Komaru finds a Future Foundation member and they give her instructions to go to a helicopter. When she gets to the helicopter, she sees a kid wearing a Monokuma head singing. She gets onto the helicopter but a Monokuma tries to enter. After she solves the issue, another issue begins. A Monokuma was up front tinkering with the helicopter controls and drives them up into the sky. Her failed execution begins, she flies into the sky and then falls to the ground but survives with minor damage to her body. A Monokuma appears in front of her then other start to surround her, she faints and wakes up in a room. The Ultimate Servant, Nagito Komaeda enters the room and asks if she could come to the main room. When she enters, five children introduce themselves as the Lil' Ultimate's. They also introduce a new type of killing game named Demon Hunting where the Lil Ultimate's had a target hitlist and it was their objective to kill all adults and make it a kids only place. Komaru's second failed execution begins, she falls down a hole with a parachute. That is where she meets Genocide/Genocider Jack/Jill/Sho/Toko. For the rest of the game, they go on misadventures to defeat the Lil' Ultimate's all together.