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The stage play is about 3 hours long and follows the same story as seen in the game. However, a few changes have been made in order to shorten the story. One of the biggest changes being that once the trial has been concluded, students who voted for the wrong person will be executed as well. Other differences from the game include: 
- All executions are performed by impaling the victims with spears.
- Kiyotaka Ishimaru dies alongside Mondo Owada because he refuses to vote him as the culprit.
- Chapter 3 gets skipped entirely; there is no money motive. Celestia Ludenberg and Hifumi Yamada are executed after the trial for the death of Sakura Ogami. The two of them had incorrectly voted Celeste as the culprit because shortly after Sakura consumed the poison, Celeste struck her with a bat.
- Most of Chapter 5 gets skipped; Mukuro Ikusaba is never presented as a murder victim, and Makoto Naegi is not nearly executed. Immediately after the survivors finish reading Sakura's letter, Kyoko Kirigiri reveals that she has found a "weapon": Alter Ego, appearing for the first time. The mastermind trial commences almost immediately.
- During the final trial, Alter Ego returns to play a video message from Jin Kirigiri.
- Junko Enoshima is not allowed to kill herself after the final trial and thus survives the killing game, on the grounds that having her stay alive would be a worse punishment for her.