Throughout his childhood he is assured by his father that the Golden Pavilion is the most beautiful building in the world, and the idea of the temple becomes a fixture in his imagination. A stammering boy from a poor household, he is friendless at his school, and takes refuge in vengeful fantasies. When a naval cadet who is visiting the school makes fun of him, he vandalises the cadet's belongings behind his back. A neighbour's girl, Uiko, becomes the target of his hatred, and when she is killed by her deserter boyfriend after she betrays him, Mizoguchi becomes convinced that his curse on her has been fulfilled.
His ill father takes him to the Kinkaku-ji for the first time in the spring of 1944, and introduces him to the Superior, Tayama Dosen. After his father's death, Mizoguchi becomes an acolyte at the temple. It is the height of the war, and there are only three acolytes, but one is his first real friend, the candid and pleasant Tsurukawa. During the 1944-5 school year, he boards at the Rinzai Academy's middle school and works at a factory, fascinated by the idea that the Golden Pavilion will inevitably be burnt to ashes in the firebombing. But the American planes avoid Kyoto, and his dream of a glorious tragedy is defeated. In May 1945, he and Tsurukawa visit Nanzen-ji. From the tower, they witness a strange scene in a room of the Tenju-an nearby: a woman in a formal kimono gives her lover a cup of tea to which she adds her own breast milk.
On the first anniversary of his father's death, he is sent to Kinkaku-ji, where his mother visits him, bringing the mortuary tablet so that the Superior can say Mass over it. She tells him that she has moved from Nariu to Kasagun, and reveals her wish that he should succeed Father Dosen as Superior at Rokuon-ji. The two ambitions -- that the temple be destroyed, or that it should be his to control -- leave him confused and ambivalent. On hearing the news of the end of the war and the Emperor's renunciation of divinity, Father Dosen calls his acolytes and tells them the fourteenth Zen story from The Gateless Gate, "Nansen kills a kitten", which leaves them bemused. Mizoguchi is bitterly disappointed by the end of hostilities, and late at night he climbs Mount Fudo, looks down on the lights of Kyoto, and pronounces a curse: "Let the darkness of my heart [...] equal the darkness of the night which encloses those countless lights!"
Kashiwagi boasts of his ability to seduce women by making them feel sorry for him -- in his words, they "fall in love with my clubfeet." He demonstrates his method to Mizoguchi by feigning a tumble in front of a girl. She helps him into her house. Mizoguchi is so disturbed that he runs away, and takes a train to the Kinkaku-ji to recover his self-assurance. In May, Kashiwagi invites him to a "picnic" at Kameyama Park, taking the girl he tricked, and another girl for Mizoguchi. When left alone with the girl, she tells him a story about a woman she knows who lost her lover during the war. He realises that the woman she is talking about must be the same one he saw two years before through a window of Tenju Hermitage. Mizoguchi's mind fills with visions of the Golden Pavilion, and he finds himself impotent. That evening a telegram arrives at the university bearing news of kindly Tsurukawa's death in a road accident. For nearly a year, Mizoguchi avoids Kashiwagi's company.
In the spring of 1948 Kashiwagi comes to visit him at the temple, and gives him a shakuhachi as a present. He takes the opportunity to demonstrate his own skill as a player. In May he asks Mizoguchi to steal some irises and cat-tails for him from the temple garden. Mizoguchi takes them to Kashiwagi's boarding-house, and while discussing the story of Nansen and the kitten, Kashiwagi starts to make an arrangement, mentioning that he is being taught ikebana by his girlfriend. Mizoguchi realises that this girlfriend must be the woman he saw at Tenju Hermitage. When she arrives, Kashiwagi breaks up with her, and they quarrel. She runs away and Mizoguchi follows, telling her that he witnessed her tragic scene two years ago. She is moved, and tries to seduce him, but again he is assailed by visions of the temple, and he is impotent.
As Mizoguchi's mental illness worsens, he neglects his studies. On 9 November 1949, the Superior reprimands him for his poor work. Mizoguchi responds by borrowing ¥3000 from Kashiwagi, who characteristically raises ¥500 of the money by taking back and selling the flute and dictionary he had given as presents. He goes to Takeisao-jinja (a shrine also known as Kenkun-jinja) and draws a mikuji lot which warns him not to travel northwest. He sets off northwest the next morning, to the region of his birth, and spends three days at Yura, where the sight of the Sea of Japan inspires him to destroy the Kinkaku.
He is retrieved by a policeman, and on his return he is met by his angry mother, who is relieved to learn that he did not steal the money he used to flee. Obsessed by the idea of arson, one day he follows a guilty-looking boy to the Sammon Gate of the Myoshin-ji, and is amazed and disappointed when the boy does not set it alight. He compiles a long list of old temples which have burnt down. By May his debt (with 10% simple interest per month) has grown to ¥5100. Kashiwagi is angry, and comes to suspect that Mizoguchi is considering suicide. On 10 June Kashiwagi complains to Father Dosen, who gives him the principal; afterwards, Kashiwagi shows letters to Mizoguchi that reveal the fact that Tsurukawa did not die in a road accident, but committed suicide over a love affair. He hopes to discourage Mizoguchi from doing anything similar. For the last time, they discuss the Zen story of Nansen and the kitten.
Finally he remembers the words from the Rinzairoku, "When you meet the Buddha, kill the Buddha", and he resolves to go ahead with his plan. He enters the Kinkaku and sets the bales on fire. He runs upstairs and tries to enter the Kukkyōchō, but the door is locked. He hammers at the door for a minute or two. Suddenly feeling that a glorious death has been "refused" him, he runs back downstairs and out of the temple, choking on the smoke. He continues running, out of the temple grounds, and up Mount Hidari Daimonji, to the north. He throws away the arsenic and knife, lights a cigarette, and watches the pavilion burn.
The acolyte's name was Hayashi Yōken, and the Superior's name was Murakami Jikai. The prostitute to whom he boasted was called Heya Teruko. Hayashi's mother threw herself in front of a train soon after the event. His sentence was reduced on account of his schizophrenia; he was released on 29 September 1955, the same year that the rebuilding commenced, and died in March 1956. (Borowitz comments that many accounts avoid giving the acolyte's name, perhaps to prevent him from becoming a celebrity.) The pavilion's interior paintings were restored much later; even the gold leaf, which was mostly all gone long before 1950, was replaced.
Mishima collected all the information he could, even visiting Hayashi in prison, and as a result the novel follows the real situation with surprising closeness.