(WARNING: SPOILERS! READ AT YOUR OWN RISK!) (I suggest watching/playing both Dangan Ronpa and Super Dangan Ronpa 2 before continuing on, or you could just bear with the spoilers.)

Makoto Naegi and his revived friends from Hope's Peak Academy and Jabberwock Island arrive at Equestria, scattered throughout the land from Ponyville to Manehattan to the Crystal Empire. It was a bit surprising at first, like when he first woke up in Hope's Peak without his intention, but after getting used to his pony body for a while, he adjusted pretty well.

Hajime Hinata, a Reserve Course student that resides in Jabberwock Island, suddenly finds himself as a pony in Equestria. Everything is new to him, from the locations to the ponies themselves–everyone seemed to be having a good time. Almost like that school field trip he was having before it turned into a despair-inducing disaster. After meeting a few new friends, he manages to get along.

However, lurking in the background is another student of Hope's Peak. When the protagonists think their work is done, they spread it even further…