Komahina

Komahina is a slash ship between Hajime Hinata and Nagito Komaeda in the game. It is well known that Hajime Hinata is indeed a bottom, but in this case he is a top. (Mettaton laughed softly at Komaeda’s adorable reaction, and pulled Komaeda up further so that his asshole was directly in front of Mettaton’s mouth.

Komaeda’s eyes widened when he realized what Mettaton was planning, and he gasped. “M-Mettaton!”

Mettaton’s robotic tongue slipped out from between his perfect silver lips, and licked the rim of Komaeda’s entrance, slurping up the cherry-flavored lube.

Komaeda could feel himself grow hot with embarrassment. He let out a squeak as Mettaton’s tongue ventured further, probing Komaeda’s walls until he found the spot which made Komaeda hiss and grasp at the sheets. He continued to torture that spot, making Komaeda squirm and moan with pleasure.) Danganronpa 2: Goodbye Despair.

Speculation
The main reason the ship sailed was because of a line Nagito Komaeda said to Hajime Hinata: "From the bottom of my heart... I am truly in love with the hope that sleeps inside you."

A line that Hajime said (in his head) in return was: "In the end, everything Nagito said... I don't know what was true and what was lies. But even so, there might have been a definite truth hidden somewhere in his words... If there wasn't, there's no way I could feel this mysterious bond between Nagito and me."

In an Otomedia poster, which was released after the anime, Nagito is seen giving Hajime a small bag of fortune cookies as a gift while they are on the ship, presumably after the anime's story. The pink hearts and the text mentioning eating cookies full of hope with "him" (using the Japanese word "kare" [彼] which means "him" or "boyfriend" depending on context), implies that it might be a romantic gesture. In the magazine's interview, Nagito is asked what autumn food reminds him of Hajime. He answers a "chestnut in its burr", comparing it to Hajime's hair, but after being told it's too normal of an answer, he goes on to explain that to properly eat one you have to go through a lot of work. He states that "Not being straightforward… it’s like Hinata-kun, right?". In turn, Hajime answers that Nagito reminds him of "the rice of a new crop" (referring to rice freshly harvested during the fall season) because of Nagito's hair's color. He also mentions that due to Nagito's "poor grip on reality", it's difficult to appoint him to a food with distinct taste.