Kokoro Connect centers on five mismatched students at Yamaboshi Academy who form the Student Cultural Society because none of the existing clubs fits them. Taichi Yaegashi, Iori Nagase, Himeko Inaba, Yui Kiriyama, and Yoshifumi Aoki soon discover that their new club has become the target of a strange supernatural phenomenon: they begin swapping bodies at random. What starts as a bizarre inconvenience quickly becomes a stressful test of trust, patience, and honesty, because each of them is forced to live through the others' routines, insecurities, and private hurts.
As the incidents continue, the group struggles to keep school life from falling apart while also facing emotions they would rather hide. The series balances school comedy with emotional drama, using the body-swapping chaos to expose fragile friendships and shifting identities. Around the Student Cultural Society, Kokoro Connect follows how these five students try to understand one another, protect the bonds they have built, and hold on to a sense of self when even their own minds cannot be trusted.