After the court martial, Willie becomes exec of the Caine and Keefer becomes captain. The rest of the officers are transferred all over the Navy in an effort to disband the mutinous crew. Maryk is sent to command a troop transport, an embarrassing assignment that signals the end of his naval career. Keefer becomes increasingly Queeg-like, isolating himself in his cabin for days at a time, and treating the crew badly. The Caine is struck by a kamikaze in Okinawa. Willie acts quickly. He runs into Keefer, who has gone to retrieve his novel. The fire reaches the deck magazines and shells begin going off. Keefer is struck in the shoulder and orders the abandonment of the ship, ignoring Willie's advice that the ship can be saved. Willie requests permission to stay aboard to try to save the ship. The captain grants it and then dives over the side with his novel.
Willie and Farrington stay on the ship. He announces that the captain gave orders to abandon, but those who want to stay can. They get the fire out and begin picking up the sailors who jumped. Keefer comes up still clutching the soggy novel. Willie turns over command. Only the sailor nicknamed Horrible has died, trapped under the kamikaze's engine. They also find the remains of the kamikaze pilot, with the skinned burned from his face in a sardonic smile. After Willie recuperates, he and Keefer talk. Keefer is distraught that he jumped, calling it one of the defining moments in his life. Keefer allows Willie to take the first twenty chapters of the novel with him to read.
At around midnight, Willie puts Keefer's manuscript down. In his near-death experience, Willie experienced a revelation: the only thing he regrets is not marrying May. He writes and sends an eight-page letter to her, apologizing and begging her to marrying him. The Caine ties up alongside the Pluto for repairs. The Caine could run at twenty knots on the two undamaged boilers, so Keefer requests permission to participate in the massive upcoming minesweeping missions. The Moulton visits them in port, and Willie meets with his old friend, and now Captain, Keggs.
Seventeen days before the war ends, the Caine gets an assignment and sweeps six mines and explodes seven. One day Willie receives a letter he hopes is from May, but it is from Ducely, who says that Queeg is assigned to a supply depot in Iowa. Willie is angry, for he knows that Queeg was not guilty. From their mooring in Okinawa, the sailors of the Caine monitor the dropping of the atomic bomb and the end of the war. They bitterly regret not playing a bigger part in the war. The end of the war also signals the end of the Caine, which is no longer worth spending millions on to repair. Willie discovers that Keefer will be released immediately, and Willie will become the last captain of the Caine. The change of command is quiet and painless.
Willie moves in to Queeg's old cabin, proud to be in command of a naval warship. He writes to May, asking if she received his letter. With time, Willie experiences all the sensations of command. He feels his senses extending to every sound and tremor of the ship. He proves himself as an expert boat handler when a typhoon rolls into the harbor. Willie goes to fleet operations to recommend taking the Caine to the states in order to avoid more typhoons. He says the Caine and the Moulton should sail back together and then be sold for scrap. Two days later, the Caine and the Moulton receive orders to sail to Bayonne, New Jersey. The sail is uneventful. In Pearl Harbor, he picks up mail, including a reprimand for his role in the Caine Mutiny, and a citation and medal for his role in the kamikaze attack. Three weeks later, on October 27, the Caine is decommissioned. Willie's mother picks him up in a new beige Cadillac, exactly as she had dropped him off more than a year ago.
Willie immediately tells his mother that he asked May to marry him. He asks if she will be upset if the marriage goes through, and she pleases him by responding, "If you're still seeking May, she must have qualities I've never had a chance to observe. Willie calls people to try to track May down. Marty Rubin asks Willie to come to his office. Willie and Marty go to a nearby hotel with a marquee advertising Marie Minotti, "Broadway's Beloved Bombshell." Marty explains May is dating the saxophonist Walter Feather. They go into the theater and Willie is shocked at May's blond hair and fierce look. May is shocked to see Willie, but she calmly introduces him to Feather. Willie and May stay in the theater alone. They argue about her hair. Willie softens and tells May that everything in the letter is still true. May says the letter was too late. Willie again asks May to marry him, telling her about nearly dying and realizing that he only regretted losing her.