In Danganronpa V3's bonus mode, Ultimate Talent Development Plan, there is an event where Ultimate Imposter brings Hifumi Yamada to Mikan after the Ultimate Fanfic Creator has been overworking on his doujins. Although the two don't interact, with Ryota knowing the techniques of Junko's brainwashing anime, Mikan being restored to her original self, Ryota being forgiven for his unintentional part in the Tragedy and the Class going to Jabberwock Island together, it can be assumed that Ryota has forgiven Mikan her attempt at raping him and the two restored their old friendship. In Hope Arc, Mikan tells Ryota to join her and their classmates in atoning for their sins. While trying to run away, Ryota is caught by a brainwashed Mikan. Her attempt is however interrupted with Junko's return, who then explains how her brainwashing anime works to the Ultimate Animator and threatens him to help her develop it further. After watching it, a brainwashed Mikan attempts to have sex with him while asking him to join her and Junko in spreading despair. He then finds a test version of Junko's despair anime on his computer. In episode 8, Ryota notices Mikan's strange behavior after seeing she's madly in love with Junko.
Going to meet with Izuru Kamukura, Junko and Mukuro leave the two together and Junko tells Ryota he can use Mikan's breasts as pillows. Mikan is moved to tears after watching it. Mikan and Ryota are glad that each other is alright and Junko suggests to watch Ryota's anime to celebrate their reunion. The Ultimate Soldier brings her to Ryota's new room that was "borrowed" from one of the trustees by Junko Enoshima.
Tsumiki then goes to Mitarai's room to search for him, only to find and be kidnapped by Mukuro Ikusaba. In episode 7, the Imposter informs Mikan about Ryota's disappearance. Mikan has been checking on Ryota's health along with the Imposter ever since.
Tsumiki is thankful for being trusted with the secret about the Ultimate Imposter taking Ryota's identity at school so that Mitarai could focus on creating his anime, and never shares it with anyone. In episode 5 of Despair Arc, Mikan nurses Ryota back to health after the Ultimate Imposter brought her to his room, being worried about his friend who was overworking on his anime and neglecting his health.