Junkomaeda

Junkomaeda is a het ship between Nagito Komaeda and Junko Enoshima in the Danganronpa series.

Canon
Prior to the Tragedy and during his suspension, Nagito learned about Junko’s plan to throw the world into despair. Wanting to test her to see if she was worthy of becoming a stepping stone for hope, Nagito devised a plan to kill her before she could spread despair.

Upon being brainwashed into becoming an Ultimate Despair, Nagito developed strange, conflicting feelings of both love and hatred for Junko and saw her as his sworn enemy. This was most likely a result of both Junko's brainwashing and Nagito's own belief that hope cannot exist without despair. In Danganronpa Another Episode, Nagito describes Junko as someone he really hates, but in the end he reveals to Monaca Towa that he both loves and hates her, and he implies that he knew her very well, or at least thinks he did. Considering his very bizarre feelings about her, it's possible that he is just fabricating and doesn't know her that well at all.

After Junko was executed, Nagito cut off his left hand and put hers in its' place. He believes he did it because of his hatred towards her and to steal some essence of her power, but it's strongly implied that he, just like the other members, obsessed over her. While talking with Izuru, he became increasingly agitated and conflicted about why he did it. When talking about AI Junko with him, Nagito appeared very excited to see her again so he may finally kill her, since he had both tried and failed to kill the real Junko.

After he awakened from his coma and his brainwashing was removed, he presumably retained his original hatred towards her and cut off her hand.

Fanon
Nagito canonically only had a crush on Hajime and wasn't really interested in girls. His conflicting feelings for Junko haven't been shown in an explicitly romantic and sexual manner, unlike Mikan's feelings. However, it was never confirmed that he didn't loved her this way too. It's possible that he became interested in her in a romantic way because of her obsession of despair - perfectly balancing his own obsession of hope.