Set in the early 20th century, Kokoro opens with a chance encounter on a beach near Tokyo that irrevocably links a young student to a man he simply calls Sensei (Teacher). Intrigued by Sensei's aloofness, the student calls upon him with increasing frequency. Eventually, Sensei and his beautiful wife open their home and their lives to him. Only later does the student learn the devastating secret that has haunted Sensei since his youth.

Aya and Hiromi are students at the same nursing school. Aya has known from a young age that she is a lesbian, and when she falls for Hiromi, the two of them end up becoming a couple. Thanks to Aya's influence, Hiromi begins to come out of her shell and stand up to her strict, controlling parents. However, her newfound rebellious streak could spell disaster for their relationship...