"Kokoro Connect" centers around five high school students in the Cultural Research Club at Yamaboshi Academy: Taichi Yaegashi, Iori Nagase, Himeko Inaba, Yoshifumi Aoki, and Yui Kiriyama. Their ordinary lives take a dramatic turn when they begin experiencing supernatural phenomena that force them to confront their deepest fears, insecurities, and emotions. The first phenomenon, known as "body-swapping," occurs unexpectedly, causing the group to randomly switch bodies with one another. This event disrupts their daily routines and forces them to navigate the challenges of living in someone else's body, leading to both humorous and deeply personal moments.

As the series progresses, the group encounters additional phenomena orchestrated by an enigmatic entity known as Heartseed. These phenomena include uncontrollable outbursts of suppressed desires, time loops, and memory loss, each designed to test their mental and emotional resilience. The characters are compelled to confront their inner struggles, such as Iori's fractured sense of identity, Himeko's fear of abandonment, Yui's trauma related to her height and self-worth, Aoki's insecurities about his feelings for Yui, and Taichi's tendency to prioritize others over himself. These challenges deepen their bonds but also expose vulnerabilities that threaten to tear the group apart.

The narrative explores themes of trust, identity, and the complexities of human relationships. The characters' interactions are marked by moments of tension, vulnerability, and growth as they learn to rely on one another and confront their personal demons. The series balances its supernatural elements with grounded, emotional storytelling, creating a compelling exploration of the characters' psyches. Through their shared experiences, the group evolves, gaining a deeper understanding of themselves and each other, even as Heartseed's interventions continue to test their resolve.