Not all of them have had canon interactions, but some of them do.
Makoto and Hajime didn't officially meet until the end of the Second game. Makoto entered the Neo world program with Kyoko Kirigiri and Byakuya Togami, and helped them leave without being turned into the ultimate despair. In the Hope Arc, Hajime helped bring Ryota under control, along with the rest of his classmates. When getting ready to leave, they blinked at each other, as to signal a farewell.
Makoto and Komaru are siblings. They would always watch TV together and talk about manga. Komaru was chosen as one of Makoto's captives in their motive videos. At the beginning of the tragedy, they were separated, with Makoto being put into the killing game, and Komaru being imprisoned in Towa city. They made contact again in ultra despair girls, where they were relieved that the other was alive. Makoto was, however, disappointed that she would be staying in Towa City. Komaru contacts Makoto during the final killing game, and Makoto promises to pick her up after the battle ends, but he never told her this. After the battle, Komaru was seen helping build the rebuilt hope's peak academy.
Kaede and Shuichi met at the start of V3, with them both being shoved into lockers. Shuichi thought that Kaede was one of the people who kidnapped him, but Kaede told him to shut up, as they were both confused. They helped each other through the hallway, until they got to the gym where they met everyone else. After their "transformation", They woke up in lockers once again, though, this time, they had talents. They accompanied each other while meeting the other Ultimates, and soon, Shuichi told her about the door he discovered. They set up cameras with the help of Miu making them, and camped in the classroom where they met. When the buzzer went off, Kaede pushed a shot put ball down the vent, and rushed downstairs. In the first trial, Shuichi was devastated when he found out Kaede did it, and was hesitant to say so. He cried and blamed himself for Kaede's actions, even though she told him it wasn't his fault. At the start of Kaede's execution, Shuichi reached out to her, trying to save her. When he figured out Kaede Hadn't killed Rantaro, but instead had been framed, he was furious. He was horrified to see their audition videos.
In ultimate talent development plan, Makoto, Shuichi, and Hajime had a discussion about gifts. Each of them prefer giving gifts rather than receiving them.
The ship sailed as a result of them all being the protagonists of Danganronpa. However, this excludes K1-B0, who is the Audience's protagonist. They are mainly shipped as friends, (Except for Shuichi and Kaede) or are shipped together as a joke. All of them have their other popular ships, like Naegiri for Makoto, Komahina and Hinanami for Hajime, Tokomaru for Komaru, and alternate ships for Kaede and Shuichi (who are frequently shipped together) like Oumasai or Saimota for Shuichi, and Amamatsu and Irumatsu for Kaede.
- Hinaegi refers to the ship just between Hajime and Makoto.
- Kaemaru refers to the ship just between Kaede and Komaru.
- Naegi Family refers to the ship just between Komaru and Makoto.
- Nakaede refers to the ship just between Kaede and Makoto.
- Saikoto refers to the ship just between Makoto and Shuichi.
- Saimatsu refers to the ship just between Kaede and Shuichi.