Kokoro is broken up into 3 sections, with the first called Sensei and I. Our narrator meets Sensei on a vacation and is drawn to him, though he does not know why exactly. They become friends. Sensei does not understand why the narrator wants to befriend him, but over time he accepts the young university student. Soon we meet Sensei's wife, a pleasant woman, and learn that the narrator's father is sick with a kidney disease. Sensei tells the narrator that his mother-in-law died of the same disease.

Once, while visiting Sensei, the narrator learns that Sensei has gone to visit the grave a friend, something he does every month. In their time together, the narrator tries to understand why Sensei does not work, nor have any friends. In a private conversation with Sensei's wife, we learn that she does not even know why, though she suspects it could be because of her. She also mentions the death of the friend as a possible cause, but she doesn't understand how one death could change a man so much. The narrator, however, successfully convinces Sensei that he wants to learn from his experiences in life, so Sensei promises to tell him eventually all about his past.

In the second section, My Parents and I, our narrator returns home as he father's illness has worsened. Before he had left, Sensei warned him to ensure that his inheritance was straightened out before his father dies. However, he is never able to bring himself to bring up the subject. His father's illness gets progressively worse until, nearly dying, our narrator receives a letter from Sensei. While glancing through it, he reads "by the time you read this I will be dead" causing the narrator to catch a train to Tokyo while his father is on the verge of death.

The third section (and the remainder of the book) is the letter Sensei wrote to the narrator, thus it is told entirely from Sensei's perspective. In the letter we learn Sensei was cheated out of his inheritance by his Uncle after his parents had both died. This began his lack of trust in humanity. However, while at university, he began to live with a widow and her daughter. Slowly, Sensei began to trust them and eventually fell in love with the daughter. At this time, he invited a friend who was struggling to live with him as well.

At first, things went well, and the friend, who was a very religious man, began to enjoy life more again. Unfortunately, the friend (K) confesses that he is in love with the daughter as well. Stricken by fear, Sensei acts cruelly and tells K that it is weak of him to love a woman and profess to be a strong-willed religious man (the sect K is a part of is celibate and considers love a weaknesses). It is clear that K is devastated by Sensei's words, but he appears to agree. Sensei, not wishing to take any chances, proceeds to ask the widow for permission to marry her daughter, and the widow agrees. K learns of this in a few days, and shortly after he kills himself.

This, confesses Sensei, is the reason he was so cold and unfeeling throughout the rest of his life. Every time he saw his wife, he was reminded of how he betrayed K. He was, he realized, not unlike his Uncle who had stolen his inheritance. His only recourse, he had concluded, was to kill himself. Which was what he planned to do now that his promise to the young narrator was kept. We are left not knowing Sensei or the father's fates as the book concludes with Sensei exacting a promise from the narrator not to tell his wife the truth.