Taking place six months after the events of Danganronpa: Trigger Happy Havoc, this game follows Komaru Naegi, the younger sister of the first game's protagonist. Komaru has just escaped from the apartment where she was imprisoned for the last year and a half, and she's emerged to find the world in shambles. She is given a special "hacking gun" by Byakuya Togami, a survivor of the killing game from the original entry in the series. This gun, shaped like a megaphone, is a weapon Komaru can use to combat the Monokuma robots that have been terrorizing those in the outside world. However, Komaru's escape goes awry, and she finds herself under attack by the Warriors of Hope, a group of elementary schoolers who wish to kill all adults and turn their current location of Towa City into a paradise for children.
Komaru forms an uneasy alliance with Toko Fukawa, a troubled girl with an intense crush on Byakuya and a murderous alternate personality called Genocide Jill. The two girls make it their goal to rescue Byakuya, who has been kidnapped by the children, and escape the city. Their journey brings them into encounters with an adult resistance group, more Monokumas, and the leader of the Warriors of Hope. Though their relationship is strained at first, Toko and Komaru eventually become close friends.
Players mainly control Komaru, who uses her hacking gun to destroy enemies and interact with the environment. When certain conditions are met, the player can choose to control Genocide Jill, whose combat abilities are more melee-oriented. Though Jill is invincible, the player's use of her is set on a timer, and they will switch back to Komaru when that timer runs out.