Naval officers begin to suspect their captain of insanity.

In 1944, at his officer training graduation, Ensign Willie Keith attempts to keep his wealthy, clingy mother from learning of his serious involvement with nightclub singer May Wynn. Disappointed, May does not see Willie off as he sails from San Francisco to the naval base at Pearl Harbor. Upon arriving in Hawaii, Willie reports to his assigned ship, the U.S.S. Caine , a beat-up, destroyer-mine sweeper, and meets cynical novelist Lt. Tom Keefer, the sober executive officer, Lt. Steve Maryk and another newcomer, Ensign Harding. Willie is unable to conceal his disappointment in the casual Capt. DeVriess and the dilapidated Caine , yet he nevertheless refuses a transfer arranged by his mother and grudgingly settles down to months of drilling of the clumsy, unkempt crew. When DeVriess is transferred, Willie anticipates the arrival of the new commanding officer, Capt. Francis Philip Queeg, coming off two years of combat duty in the Atlantic. Although mystified by the crew's sentimental send-off of DeVriess, Willie is pleased with Queeg's brisk, if peculiar, manner. Queeg appoints Willie morale officer and immediately orders the Caine thoroughly cleaned up. A few days later, after a standard target practice exercise, Willie is summoned to the bridge to be reproached by the captain for not punishing a disheveled sailor. Queeg becomes so engrossed in the reprimand that the Caine steams undirected in a circle, severing its target tow-line. The incident results in the Caine being summoned back to San Francisco, where Willie goes to see May and presents her to his anxious mother. Willie takes May to Yosemite and proposes, but May refuses, claiming that Willie is still too concerned about his mother's opinions. Shortly after returning to sea, the Caine is ordered to escort assault teams to enemy-held beaches, but during the first mission, Steve is forced to take temporary command when Queeg is inexplicably absent. When the captain finally arrives, he grows anxious at the enemy shelling and alarmed as Steve slows the ship to protect the smaller landing craft. Queeg orders the Caine to drop its yellow dye marker to indicate the landing zone, then to retreat to open sea. Willie is perplexed by the captain's behavior, while Tom makes sarcastic comments about Queeg's bravery. Later, Steve sternly rebukes several officers, including Tom, Willie and Harding, for making up a song, "Yellowstain Blues," which besmirches Queeg. Willie is bitterly disappointed by Queeg's character lapse, but neither he nor any of the officers respond when Queeg makes a thinly veiled request for support. When Tom observes that Queeg's eccentric mannerisms and increasingly irrational behavior indicates that he is mentally unsound, Steve demands that he take the charge to the medical officer, but Tom refuses. Disturbed by Tom's suggestion, however, Steve gets a book on mental illness from the ship's library and begins keeping a log of Queeg's escalating erratic behavior, which has begun to sap the crew's morale. Late one night, Queeg summons all the officers to begin an investigation of the disappearance of a gallon of strawberries from the mess. When the lengthy inquiry extends to searching each crew member for a duplicate mess key that Queeg is certain must have been used in the theft, Tom reiterates his challenge of Queeg's mental soundness and suggests Steve consider relieving the captain according to Navy regulations. Steve is further upset when Harding, who must leave the ship to attend his seriously ill wife, reveals that he witnessed the mess boys eating the strawberries and reported the incident to Queeg, but the captain threatened to cancel Harding's emergency leave if he repeated the story. Steve then asks Tom and Willie to accompany him to fleet commander Admiral Halsey to seek advice. On board Halsey's carrier, Tom reconsiders, cautioning Steve that he may ruin his career by accusing Queeg. Uncertain, Steve acquiesces and the men return to the Caine . The fleet is then ordered out to sea into a strong storm, during which Queeg risks capsizing the Caine by stubbornly maintaining the ordered course, despite Steve's pleas to turn the ship. When Queeg appears terrified by the violent pitching of the ship, Steve, fearful for the ship's safety, relieves him of command using the Navy code. Willie supports Steve, and Queeg's order for their arrest is ignored by the other officers. Some time later, in San Francisco, May telephones her support to Willie, as he and Steve are brought up for court-martial. Cynical Lt. Barney Greenwald is the only lawyer who grudgingly accepts Willie and Steve's case. At the trial the prosecution is led by Lt. Cmdr. Challee, who establishes Willie's naval inexperience and gradual loathing of Queeg. Testimony offered by other sailors reveals only that Queeg was a demanding, driven commander. Under questioning, Tom admits that he was not present at many of Queeg's supposed displays of unstable behavior and lies that he had not suggested to Steve that Queeg might be mentally unfit. Tom then goes on to say that he does not believe Steve's log holds enough information to justify the mutiny. A naval psychiatrist asserts that Queeg is not mentally ill, but under Barney's probing admits that the captain suffers from deep paranoia due to long and arduous combat duty. When Queeg takes the stand, he severely criticizes Steve, yet is unable to explain his earlier positive written evaluation of his executive officer. Barney brings up the tow-line and dye stain incidents, but Queeg insists his officers were disloyal and unsupportive. Queeg grows increasingly agitated when Barney mentions the missing strawberries and when Harding's name is brought up, the captain takes up his nervous habit of rolling metal balls in his hand and launches into a lengthy, rambling defense. In the face of Queeg's obvious instability, Steve and Willie are acquitted. Afterward, during the celebration with the Caine 's officers, a drunken Barney chastises them for not supporting Queeg and for putting the ship in danger by their recklessness. The men are startled when Barney accuses Tom of being the true instigator of the Caine mutiny. Soon after, Willie and May marry and, upon returning from their honeymoon, Willie reports to his new ship to discover, with a sense of relief, that his commanding officer is DeVriess.