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The game starts out identically to the beginning of the main story, where Makoto Naegi enters the school and passes out. However, Makoto does not wake up in an empty classroom and instead wakes up at the sealed exit room along with some of the other students. After briefly discussing their situation, the group leaves towards the gym, where they meet with the rest of the students and Monokuma.
Once again, Monokuma makes an identical announcement like from the main story, however he declares that he is currently at a loss on what to do since he has forgotten to create "backups" for himself, and therefore cannot truly begin the group's "School Life". Although all the students are confused and reluctant to go along with Monokuma's words, he reminds the group that the door is sealed and that there is currently no way to leave. Monokuma then announces that in order to "trigger the escape flag", the students must work together to create backups based on his specifications. After he leaves, the students all reluctantly agree to go along with Monokuma's orders since there was no telling what could happen if they refuse.
The player now has 50 days to build the assigned backups for Monokuma. The player may either spend time assigning students to either gather materials, rest for the day, or clean the school. Gathering materials will slowly consume each student's energy, as well as slowly make the school messier. Resting for the day will not provide materials to build backups, but it will also prevent the "Cleanliness" gauge from rising any faster. Cleaning will also take energy, but the "Cleanliness" gauge will increase. If the "Cleanliness" gauge becomes empty, Monokuma will force the students to clean the entire school, wasting a few days. Also, the player will be given the opportunity to raise Makoto's "relationship" with another student. If the player manages to build the assigned backup, Monokuma will provide the player with Monokuma Tickets, which can be used to take another student on a "date".
After reaching the 51st day, if the player manages to build every backup assigned, the students will all gather around Monokuma, who yells at them for making a "backup" that doesn't even look like him. Out of anger and frustration, Monokuma decides to punish Makoto, saying that it would "motivate" the other students to do a better job next time, but the "backup" suddenly comes to life, introducing itself as "Usami". After a small argument, Usami attacks Monokuma until he agrees to release the group and gives them the escape button before disappearing. Usami then thanks the group and says goodbye before mysteriously shutting down. Although many of the students are still confused, the group happily makes a small celebration as they are finally allowed to leave at last.
If the player manages to max out Makoto's relationship to another student, there will be a small scene available at the end where Makoto may speak to one of the other students before receiving a "special gift".
Monokuma requests that the students build spares from the materials around the school. Below is the list of spares.
- Casanova Monokuma
- Monokuma Butler
- Monokuma Entertainment System
- Cooking Mamakuma
- Eco Monokuma
- Moe Moekuma
- Monokuma Savant
- Heavy Arms Monokuma
- Warlockuma (Usami)
Trigger Happy Heart
Trigger Happy Heart is a minigame in School mode. It uses mechanics used in the Rapid Fire Debate trial minigame in the main plot. After gaining a "Trip Ticket" from Monokuma and using it to go on a trip with another student, Makoto is given an insight into their mind and is given the ability to reply to the student's thoughts by shooting an "Affirmation" or "Negation" bullet. It is much like the "Shot Through The Heart" minigame in the Island mode of Danganronpa 2. Replying to the right thoughts with the right responses will earn a step forward towards getting their ending.
Unlike the Rapid Fire Debate, there is no time limit on Trigger Happy Heart.
- During the introduction and the end, Monokuma will break the fourth wall by referencing how he was destroyed during the Prologue and Chapter 5, and how certain events weren't supposed to happen until the sequel.
- During Sayaka Maizono's ending, Makoto will have flashes of events from the main story involving him and Sayaka, who also seems to remember said events. This seems to imply that Sayaka really does have a limited amount of psychic ability.