While under the influence of the despair disease in Chapter 3, Mikan recovered her memories of school life. At the end of the trial that unveiled her identity as the culprit, she revealed that she did it for the sake of 'her beloved', claiming that they forgave and accepted her for who she was, in stark contrast to the maltreatment she had been exposed to her entire life, and that they would appreciate her actions if they were alive.
Mikan proceeds to ramble feverishly about how their love transcends the cruelty of her misdeeds, and how this person was a major factor in her drastic personality change. Due to her wording and the circumstances of her past, it is heavily implied that this person is Junko, who may have brainwashed her.
This is later confirmed in Danganronpa 3 - Side: Despair where their relationship is revealed. Mikan is brainwashed by Junko, and acted towards her in a way similar to Mukuro Ikusaba, only much more insane and unnatural. She is glad when Junko abuses her or gives her attention, and learns to share Junko's love of despair.
However, Mikan later returns to her original state, before the brainwashing, no longer holding these feelings for Junko and even assisting the Future Foundation in wiping out despair.
In one event in Danganronpa V3's bonus mode, Ultimate Talent Development Plan, Junko visits Mikan in the nurse's office and wants to chat with her out of boredom. Mikan is at first reluctant as the nurse's office is supposed for treating the patients rather than conversations, but Junko tricks her into starting one by asking if she doesn't want to talk with her. She then suggests talking about Mikan's classmates as she might find this information useful in the future, which is a callback to their interaction in Despair Arc.
- “What I did...was for the sake of my beloved. If only they were still alive...”
- — Despair Mikan committing double murder in Chapter 3 of Danganronpa 2 for Junko Enoshima.
- “My beloved...was the only one... That's right, the only one who... ...never hated me. They forgave my existence. They forgave me and accepted me. They gave me value. They loved me. I loved them with all my heart and they returned it in full. This is...my reciprocation.”
- — Despair Mikan about (how she views) her relationship with Junko.
- “Even so...the current me was most strongly influenced by my beloved's existence. And it was also my beloved who created the me that everyone can't forgive. But my beloved still forgives me and still accepts me... That is the key difference between all of you and my beloved.”
- — Despair Mikan about being strongly influenced by Junko.
With Despair Mikan mentioning "her beloved" in Danganronpa 2's Chapter 3 and saying how they were the only person to forgive her existence and show her love and affection, many fans were curious about who the mysterious beloved could be. With Nagito calling the current version of Mikan worthy of the name "Ultimate Despair" and Mikan mentioning that her beloved is already dead, some suspected it was Junko. Those suspicions were later indirectly confirmed in Chapter 6 where the entire Danganronpa 2 cast was revealed to have been members of the Ultimate Despair.
With this reveal, fans were curious to see whether Junko indeed treated Mikan nicely, and if so whether that was to manipulate her into joining Ultimate Despairs. Knowing it was Junko, some fans were worried. Their worries were confirmed in Despair Arc, where Mikan was bainwashed by Junko's early version of Despair Video, and where Junko abused her both verbally and physically.
Thus, it was confirmed that Mikan only interpreted it as affection because of being brainwashed, as well as because of her belief that it's better to be abused than neglected. As a result, a majority of the shippers have abandoned the ship, resulting in it going from one of the more popular to one of the least popular ships.
Some fan fictions tend to use the early predictions and abandon the idea of Junko brainwashing Mikan, instead making her actually act nice to Mikan in order to manipulate her into joining her.