Like its predecessor, Super Danganronpa 2 is a murder-mystery visual novel with action elements. The player character this time is Hajime Hinata, a new student at the elite Hope’s Peak Academy. On his first day at the Academy, his class meets Usami, a pink rabbit who dresses like a magical girl and introduces herself as the students’ teacher. She transports the kids to Jabberwock Island, an uninhabited tropical paradise, tells them that they are now on a class trip, and instructs them to befriend one another and collect hope fragments. But just as the students are getting used to their bizarre new situation, the sadistic Monokuma appears and throws them into a game of life and death.
Once again, the Hope’s Peak students can only escape the island if one of them is able to murder a classmate without being caught. Once a murder takes place, a class trial will be held to decide the guilty party. If the murderer is not correctly decided upon, that student will be able to leave at the cost of everyone else’s lives. However, if the students do find the culprit, that single person will be messily executed in an elaborate display.
The game is divided into six chapters, which are further broken into Daily Life and Deadly Life segments. In Daily Life, the player can engage in Free Time conversations, in which Hajime gets to know his classmates by selecting the correct options in their dialogue trees. Completing Free Time awards Skill Points that can be spent for various beneficial abilities during trials. This part of the game also includes exploration of Jabberwock Island and scripted scenes. Once a murder has been committed, Deadly Life begins, and Hajime must scour the island for evidence during the Investigation. When all evidence has been collected, the game switches to the Class Trial, a fully-voiced set of cutscenes and action-oriented minigames. The player must then use both their reflexes and logic to present the correct evidence, debate with other students, and draw the conclusions that will expose the true murderer.
An alternate mode called Island Mode is unlocked after beating the main game. It presents an alternate universe in which Monokuma does not sabotage the class trip, and the students collect the hope fragments as per the original plan. Free Time conversations may also occur in this game mode, as well as brand-new scenes for each character.