Mukuro is Junko's older twin sister. While Mukuro cared deeply for her younger sister, Junko had absolutely no love for her sister and sees her as a tool to do her bidding, while at the same time behaved towards Mukuro in a derogatory manner. Mukuro viewed Junko as being far superior to her and would do anything to earn her praise, even going so far as to join Ultimate Despair and taking part in the School Life of Mutual Killing. Junko made it very clear that she believed herself to be superior to her older sister too and criticized her on several occasions. Mukuro took her sister's insults to heart and believed Junko was always right.
Junko was verbally abusive and cruel towards Mukuro. She seemingly displayed no concern for Mukuro and was willing to kill her (while Mukuro was disguised as her) to set an example to the remaining students, and because she was 'a poor actor'. It's revealed that before attending Hope's Peak Academy, Junko had already tried to kill Mukuro. One example of this is when Junko tried to murder her sister with an ice pick and a grenade while in a limo. Mukuro, however, did not allow her to do this, blocked Junko's attacks, and threw the grenade out the window. Still, Mukuro understood that Junko was trying to taste the despair of killing her own sister, and was actually happy to know Junko would fall into despair by murdering her.
However, paradoxically, it was also indicated that Junko did truly love her sister and that her betrayal was meant to send them both into despair (for Junko, the despair of killing her sister, and for Mukuro, the despair of being betrayed and killed by her sister). However, Junko never knew, or tried to understand, that Mukuro's definition of despair had always differed from hers.
Mukuro wanted nothing more than for Junko to be happy and to be loved by her, but was aware that she did not subscribe to the same notions of despair compared to her sister. She refused to leave her side though, as she believes no one else besides her can truly understand her sister.
When Mukuro talks or thinks about her sister in Danganronpa/Zero and Danganronpa 3, she sometimes blushes and appears to be in a state of ecstasy, implying that she has incestious feelings for her sister. In Danganronpa/Zero, she turns ecstatic and feverish as she explains Junko's relationship with her and despair, considering her own relationship with Junko special because she truly is the only one who understands her. She claims that is why Junko needs her, though she hasn't realized it yet. Acting giddy, Mukuro thinks that maybe Junko just pretends not to realize it because she is "so shy". Hearing all of this, Ryouko is disturbed and concludes that Mukuro's feelings for her sister are definitely not normal.
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