Upon the start of the game, Shuichi Saihara woke up inside a locker of an eerie classroom with overgrown vegetation and futuristic motifs such as an expensive looking monitor and blackboard. After stumbling out of the locker, Shuichi was greeted by another person around his age, who quickly introduced herself as Kaede Akamatsu. Frightened and confused, the duo quickly realized that it would be impossible to learn anything by sitting around in the classroom, and so they decided to explore their surroundings and exited the classroom into a hallway. However, a large robot called an Exisal was waiting for them and, unbeknownst to the couple, this Exisal was leading them to the gymnasium were fourteen other students had already gathered.
After encountering the fourteen other students in the gym, Shuichi and Kaede proved to be even more confused than before. Shuichi would only be faced with more questions than answers as all five Exisals appeared in the gym, beginning to threaten the group of students. Eventually, the ones controlling the Exisals realized that they had gone off-script and weren’t supposed to be using the Exisals just yet. Thus, the five controlling the Exisals exited the robots, introducing themselves as the Monokuma Kubs. The Kubs distributed sixteen new uniforms to the students, replacing their generic school uniforms so they can look more like "Ultimates." After everyone is dressed in their new attire, the Kubs give the sixteen students their first memory via the Flashback Light. Shuichi and the other fifteen talentless students underwent the fabrication process, where all of their past memories and personalities were erased and replaced with entirely new, fictional ones. Shuichi, and the other fifteen students, also received Ultimate talents, with Shuichi being given the title of Ultimate Detective. All of this was done for the sake of Team Danganronpa’s audience, so the Killing Game would be more interesting. After the fabrication process was completed, Shuichi and the others entered the Ultimate Academy for Gifted Juveniles as totally different people, officially commencing the 53rd Killing Game season known as the Killing School Semester.
Shuichi once again woke up in the same locker as before, along with Kaede. The two had no recollection of their previous meeting and as such, reintroduced themselves, both now under the impression that they were Ultimate students due to the new memory they had been given. Kaede believed herself to be the Ultimate Pianist, and Shuichi believed himself to be the Ultimate Detective. The pair explored the seemingly abandoned school, finding and introducing themselves to all fourteen other students before being told by the Monokuma Kubs to assemble at the gymnasium. Kaede and Shuichi, along with everyone else, headed there immediately and were introduced to the Monokuma Kubs properly, along with their father, the self-appointed headmaster of the Ultimate Academy for Gifted Juveniles, Monokuma. Monokuma announces that all sixteen Ultimate students would participate in a Killing Game, much to a majority of the students shock, horror, or displeasure. With the students’ complaints falling on deaf ears, the Killing Game had officially begun.