The novel begins with the unnamed protagonist writing about his past experiences with a man whom he called "Sensei" ("teacher" in Japanese). During a summer holiday at the beaches of Kamakura, a city near Tokyo, the narrator, then a university student, is left alone when his friend is forced to return home. While aimlessly frequenting the beach alone, he notices and then befriends an enigmatic older man, whom he impulsively calls Sensei. Back in Tokyo, he calls on Sensei, but finds that the man has gone to a nearby cemetery at Zoshigaya and so he follows him. Sensei is uncomfortably surprised to see the narrator, and, refusing to reveal the full significance of the graveyard he visits monthly, only tells him that a friend of his is buried there.
The narrator begins to visit Sensei more often and, his respect and interest in the man growing with each of their conversations, he tries to come to an understanding of him. Though Sensei lives comfortably with a beautiful wife, Shizu, who is the like the ideal of a kind and obedient spouse, he is intensely melancholic and reclusive, and often speaks critically of himself, alluding to what the narrator discerns is a past tragedy while concealing most details. Moreover, despite the strong love that exists between Sensei and his wife, the narrator learns from one occasion when he hears Sensei having an argument with her that Sensei feels she will never completely understand him. One day while walking in a park, Sensei tells the student enigmatically about guilt in love, but refuses to explain further.
Over time, the narrator becomes the most regular guest at Sensei's quiet household, and one evening he stays there alone with Sensei's wife in order to protect her in Sensei's absence. The two begin to talk about Sensei, and the student wonders about the relationship between Sensei's general weariness for the world and his love for his wife. Sensei's wife says she believes Sensei must dislike her too, because she is part of the world he dislikes, but the narrator disagrees and senses that even she does not believe this. Then Sensei's wife, with tears in her eyes, asks the narrator whether he thinks she is to blame for Sensei's unhappiness; the narrator disagrees to this too, which prompts Sensei's wife to recall the incident in Sensei's past after which he changed from an energetic young man to a melancholic: a student friend of his died, and not by natural cause. However, out of modesty, she refuses to elaborate, and the two leave the matter when Sensei returns.
The narrative frame of the entire story is the unnamed narrator writing about his experiences with Sensei an unknown length of time after Sensei's suicide. As such, over the course of the story he makes many references, some more explicit than others, to Sensei's end, and steps back from the story itself to comment on how he had not at the time realized the significance of a certain event or something that Sensei said. This detached, almost critical eye with which the narrator retells his own story, that is to say his memory, becomes very much the viewpoint that the reader takes. Indeed, we wonder along with the narrator in his younger days about this mysterious man Sensei, trying to figure out what his dark past is. In a sense, the book is a mystery novel, and fittingly, it contains something close to a murder.
The novel opens with many important elements that will return over the course of the story, including notable parallels in Sensei's testament. For example, the narrator's friend leaves after receiving word of his mother's sickness (just as the narrator will be called back home due to his father's sickness and Sensei's mother-in-law will fall sick), though at the same time he suspects that they are trying to force him into a marriage (just as Sensei's uncle tried to force him into a marriage) and feels that he is too young because of his modern outlook (such as what the narrator himself holds). Furthermore, many scenes from the narrator's encounter with Sensei at swimming at the beach will be repeated, such as in Sensei's description of his friendship with K. Another interesting detail, that the narrator first noticed Sensei because he was with a Westerner, announces the theme of cultural conflict between East and West early on.
Although the narrator considers himself a thoroughly modern and rational person, he nevertheless is drawn to Sensei by a strong sense of intuition, something from the heart instead of the brain, which is perhaps similar to kind of thinking he attributes to women. Moreover, the narrator makes a point that he does not treat Sensei in a cold intellectual way, just as he later says that he does not consider Sensei a great man in a "intellectual" but a "spiritual" sense. His conversations with Sensei always focus on how one lives a proper life, but rather than drifting into abstract philosophizing, the discussions are invariably rooted in Sensei's personal experiences, although he does not reveal them. From the enigmatic things that Sensei says, the narrator learns life lessons and about the man himself, though very much implicitly. For one, he intuits that Sensei is a man "who was by nature incapable of not loving" (12).
One of the most significant things that Sensei says in his early discussions with the narrator is that "Loneliness is the price we have to pay for being born in this modern age, so full of freedom, independence, and our own egotistical selves" (30). As the rest of the story shows, loneliness is one of the main problems which humanity faces, and it is a problem specifically grounded in the Western modernity which has extended its influence into traditional Japan. Despite the torment that it causes Sensei and the narrator, or perhaps because of that, loneliness serves to draw the two of them to each other. In a word, loneliness is closely associated with the problem of communication and interpersonal understanding, so a mutual recognition of the struggle with understanding others and being understood oneself makes Sensei an interesting teacher to the narrator (certainly more interesting than his university lecturers) and the narrator a worthy audience for Sensei's retelling of his life's anguish.
Though the narrator and likely the readers too do not at first notice it, many of Sensei's words are filled with a heavy foreboding. At times the narrator makes this clearer by his own editorializing, such as when he writes, "The grave stood like some monstrous thing, forever separating us" (32). But when Sensei blurts out that it is because of "divine punishment" that he and his wife will never have children, and the narrator does not comment, the reader may not realize that Sensei is alluding to a past crime that he feels he has committed. Nevertheless, the discussions about his friend's grave at Zoshigaya and unnatural ways to die (suicide and murder) foreshadow Sensei's later revelation.