Once Soseki boards the train, he re-opens Sensei's letter. Frantic, Soseki sneaks out of the house and hastens his way to the train station praying his father will be alive when he returns from Tokyo and that Sensei will be alive when he arrives there.

Soseki searches the pages for answers but finds nothing that satisfies him. Distracted with worry, Soseki only glances over the letter until he reaches the end and realizes Sensei has decided to kill himself. Soseki is tending to his father when his brother hands him a letter from Sensei.

When he begins suffering fainting spells and nausea, Soseki is reminded of Shizu's mother and believes his father's death is not far off. Shortly after Emperor Meiji falls ill, Soseki's father's illness takes a turn for the worse. When Soseki arrives home after graduation to find his father actively working in the garden, he is haunted by Sensei's and Shizu's words of caution and is filled with worry. Soon however, he is bored of the country and finds himself continually comparing his father unfavorably with Sensei. When Soseki is home with his parents he is initially happy to be with them. Sensei acquiesces saying he will tell his life story when the time is right. Sensei is unsure he can trust Soseki, but the younger man assures him he is a true friend. Soseki also feels that Sensei has erected a wall between them and one day confronts Sensei with his suspicions. Shizu loves her husband, but Sensei hides what torments him and has spent their wedded life just outside of her emotional reach. Shizu explains to Soseki that a friend's unnatural death coincided with the slow descent Sensei has taken into isolation. Soseki learns more about Sensei through his wife, Shizu and his knowledge and feelings for her grow as well. Often Soseki is confused and disappointed by Sensei's words and believes the older man's perceptions of him incorrect. Sensei believes Soseki has sought him out because he is lonely, but himself unworthy of society and unable to help the younger man. Soseki is a young man bored with life when he befriends Sensei. Kokoro is a tale that gets to the heart of the loneliness, fear, and guilt that accompanies love, individuality, and betrayal. Only when Sensei decides to end his life does he decide it is time to pass on his testament. Though Soseki and Sensei develop a close friendship, Sensei's life remains a mystery.

What Soseki does learn is that Sensei is a troubled and reclusive man who does not trust himself or humanity enough to interact with the world. Soseki befriends an older man he calls 'Sensei' with the expectation of learning about life. It is the story of many individuals who long to appease loneliness, and the story of two men who attempt to assuage loneliness through love but only find peace in death. Kokoro is a story of one young man searching to fill a void in his life.

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