While there were no real interactions between the two in the first game, their relationship is explored and elaborated on in the novel Danganronpa IF.
It is revealed that they were friends due to being classmates, though seemingly not very close due to Mukuro's distant personality. Mukuro was in love with Makoto due to him being the first person to ever smile at her, though he appeared to be unaware of this and thought of her as a friend. She would often watch him from afar while they still attended Hope's Peak before The Tragedy occurred, as she lacked the courage to tell him how she felt. Another hint at her crush is provided in the first game, as during the last class trial when some group pictures of Class 78th are shown, Mukuro is looking away from the camera (some appear to be deliberate). However, the only one where she is actually looking directly at the camera is the one taken by Makoto. In Danganronpa IF, Junko says that Mukuro never cared about being in the photos, but did care about the one Makoto was taking.
It was because of Makoto that Mukuro began to think more of the world outside of Junko's plans, and it caused her to have doubts when Junko revealed her plan for the killing game involving their fellow students, Makoto included. However, initially, she was perfectly willing to kill him if for Junko's sake, despite the way she felt about him. As shown in Danganronpa 3, Mukuro hesitantly suggested that she and Junko kill Makoto immediately after her sister deemed him a threat.
In Danganronpa IFs alternative universe, this changed drastically after Makoto became heavily lacerated for saving Mukuro where she became desperate in saving a moribund Makoto. As Junko then gives Mukuro the injunction to kill Makoto, Mukuro responded in refusal. Makoto treated Mukuro very kindly and placed his trust in her, even after it was revealed she was partly responsible for what had happened to Hope's Peak Academy.
The ship isn't too well known due to originating from a side material, Danganronpa: IF light novel included as a bonus feature after completing Danganronpa 2. For a ship originating from a side material, it has a large number of shippers. It was popular enough to warrant being referenced in the OVA. It sailed as a result of Mukuro Ikusaba developing a crush on Makoto.
- Makoto's relationship with Mukuro on Danganronpa Wiki
- Mukuro's relationship with Makoto on Danganronpa Wiki