Komaru is Makoto's little sister. Being one of the closest people to him, Makoto loves her dearly, which is proved when she is chosen as Makoto's Captive. They are also slightly similar as siblings, as they both have the same ahoge. According to Komaru, the two watch TV together, as well as share thoughts on manga they share with each other. She's also mentioned that they did argue quite a bit, which is a rather common occurrence between siblings.
When the Tragedy began, Makoto was separated from his sister and forced to participate in the Killing School Life. In an attempt to persuade the participants to kill someone, Monokuma gives them videos showing the people they cared about most get hurt or killed. In Makoto's video, Komaru and their parents were in their home congratulating him on getting into Hope's Peak Academy, but suddenly disappear from their place on the couch, which has been destroyed as well as their home. Makoto was terrified, now believing that Komaru and their parents were dead, and was desperate to get out. However, when he learns Komaru is alive, he was greatly relieved and ecstatic to see his sister again. He was a bit disappointed when she informs him that she would be staying in Towa City.
Makoto is once again contacted by Komaru during the Final Killing Game. Makoto almost despairs when he learns from Komaru that one of his friends would die because of him, but Komaru reminds Makoto that he has to stay alive so he could pick her up. This gives Makoto hope, knowing that his sister and friends were supporting him, and proudly takes notice of Komaru's growth. Although Makoto does not get a chance to tell her, he swears that he will pick Komaru up after his battle ends.
After the battle ends, Makoto supposedly reunites with his sister (although this is not shown on screen), who assists him and his fellow survivors in rebuilding Hope's Peak Academy.
The familyship sailed as a result of the two canonically being siblings. It is rarely shipped as an incest relationship, especially because both characters have their much more popular romantic ships, such as Tokomaru or Naegiri.
- Both were the main protagonists in Danganronpa franchise at least once, with Makoto being the protagonist of Danganronpa 1 and Future Arc and Komaru being the protagonist of Danganronpa Another Episode: Ultra Despair Girls.