Queeg's ban on water becomes painful on the trip to Funafuti when a tail wind makes the stack exhaust hover in a cloud around the ship. All day, the sailors' tongues are coated with a thick, itchy, foul-tasting film, and the desire for water becomes unbearable. Maryk begs the captain for a reprieve, but Queeg will not grant it. The next day the heat and wind continue to torture the crew. Finally, the engine room crew starts bootlegging water from the engine compartment. The officers suffer on in agony while the sailors enjoy their ingenuity. Willie hears a shriek from Queeg, who has found the new ensign, Jorgensen, with his shoulders wet with water. The sailors' ban is lifted at five that evening, but the officers are restricted from using water for another forty-eight hours.
When the Caine reaches Funafuti Atoll, it ties up to a destroyer tender ship called the Pluto. Destroyer tenders provide fuel, water, fresh breads, and fruits for the Navy. Willie runs into Ensign Acres, now Lieutenant jg Acres, who is no longer good looking, as he used to be. The former instructor at Furnald is more than forty pounds overweight. Willie learns that after his stint as an instructor, Acres put in for duty on the tender and married. Willie does most of his back work in the Pluto's communication's office. Acres informs Willie that Willie had made Lieutenant jg with the class of February. Willie goes with the officer to buy new silver collar pins. When Willie returns to the Caine, he decides not to report the water ban to the Pluto's chaplain. He notices how lean he looks and feels a twinge of pride in his difficult life.
Queeg made an inquiry about the health of Stilwell's mother, and the response comes. Maryk tells Willie that the captain has planned a court-martial. Willie is to be the recorder of the proceedings. Queeg congratulates Willie and officially endorses his promotion to Lieutenant jg. He explains how to record a court martial, and reveals his hope that Stilwell will be discharged by the court, producing a confession that he forced from Stilwell earlier. Willie studies Courts and Boards, especially the section on confessions, and convinces Stilwell to plead not guilty. Willie is sure he can get the confession thrown out on grounds that it was forced from Stillwell under duress. The next morning, Stilwell tells Willie he talked to the yeoman aboard the Pluto, who was a lawyer in civilian life, and the yeoman convinced him he could be found not guilty. When Willie reports to the captain that Stilwell plans on pleading not guilty, Queeg throws a fit. He immediately sends for Stilwell and when the sailor emerges an hour later, he explains that he will be pleading guilty, and volunteers a new affidavit reading that he had volunteered the confession in no state of duress.
The next day, the four officers of the court, Willie, Maryk, Keefer, and Harding, drink beer until the two o'clock scheduled start of the trial. Keefer, as usual, tries to convince the others of the captain's unsound mind, but Maryk will not hear it. The court hears Stilwell's confession and the jury of Keefer, Paynter, and Harding find the defendant guilty of the charges put forth against him, but only sentence him to the loss of six liberties. They sullenly send up the verdict to Queeg's cabin and wait for the expected response. Five minutes after the end of the trial, Queeg calls a meeting of all officers and berates them for their insubordination. He promises to make them pay for every mistake in their performances and assures them of the poorest possible fitness reports.
Later, Maryk and Keefer discuss the captain's mental state in earnest. Maryk asks Keefer if he would be willing to present their theories on the captain's insanity to the Pluto's medical officer. Keefer balks, and Maryk says, "All right, Tom. That was a request to put up or shut up." Since Keefer is unwilling to act on all his talk, Maryk will no longer allow him to spread his malicious views of the captain. Keefer is silenced. Maryk leaves and retires to his cabin, where he reads a borrowed copy of Mental Disorders.
As the Caine steams from Funafuti for Noumea, it becomes known among the officers that Maryk was writing in his bunk late at night. People speculate on the subject of his writing, but no one guesses the truth. Maryk is keeping a log called "Medical Log on Lieutenant Commander Queeg," marking down all Queeg's daily habits, his sporadic outbursts, and his moods. Maryk's log grew thicker during all the months the Caine bounced around the islands of the Southwest Pacific. Maryk's log chronicles that every time Captain Queeg emerged from his cabin, something awful resulted: Queeg cut off water, coffee, or movies, and announced reductions in everyone's fitness reports.