Naejunko

Naejunko is the het ship between Makoto Naegi and Junko Enoshima from the Danganronpa fandom.

Canon
As the Ultimate Hope, Makoto was a major enemy of Junko. In turn, she seems to be one of the few people he genuinely dislikes, as he's usually very kind and forgiving. In turn, Junko thinks out of all the students in Class 78th, Makoto seems to be the most annoying and odd person in her class.

They developed a great hatred for each other during the mutual killing game. In the end with the help of his friends, he had Junko Enoshima executed. However, even in her case, he felt that she didn't need to die and tried to reason with her when she was about to execute herself. Though dead, Junko has found ways to antagonize Makoto through her AI form.

Besides his hatred for Junko, in Danganronpa IF, after he convinced Mukuro Ikusaba to think outside of Junko's world, he said that he would try to convince Junko in the same way as her sister, even after it's revealed that she's the mastermind of the Killing game.

Fanon
The ship sailed as a Foe Yay type of ship. It came as a result of them being polar opposites, with Makoto being the protagonist of Danganronpa 1 and Junko being the antagonist, as well as with Makoto being the Ultimate Hope against Junko's Ultimate Despair.

Fandom
AO3

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Trivia

 * Both, along with Byakuya Togami, Monokuma and Usami, are the only characters who appeared in every main installement of the series in one way or another.
 * In their case, they were the main characters of Danganronpa 1, appeared in the finale of Danganronpa 2, appeared in Ultra Despair Girls (although Makoto only via a laptop's screen and Junko only via flashbacks), both appeared in two arcs of Danganronpa 3 (with Makoto also appearing in Hope Arc), and appeared in New Danganronpa V3 (through Tsumugi's cosplays and through one Flashback Light each in the main plot, as well as in person in the bonus mode Ultimate Talent Development Plan).