The Caine returns to the Ulithi Atoll. The battleship New Jersey joins it in port, and Maryk notices that the New Jersey flies the four stars of the fleet command, indicating that Admiral Hasley is onboard. Later that day, Maryk and Keefer take the gig to the New Jersey, planning on giving their report on Captain Queeg to the admiral. The two officers are awed by the New Jersey's towering superstructure. Keefer has second thoughts, but Maryk presses onward. They stumble across Admiral Hasley's quarters. Maryk wants to barge in and talk to the admiral, but Keefer stops him. He says that since setting foot on the New Jersey, he sees the case in a whole different light. Keefer is afraid that the captain's actions will appear to be those of a good, strict captain. Maryk accuses Keefer of being afraid, and Keefer admits it. The officers return to the gig.
While the Caine sits in Ulithi Atoll, the largest naval force the planet has ever seen assembles around it for the assault on Luzon in the Philippines. To stave off boredom, Willie begins to study some navigation from Maryk, and ends up taking over plotting hurricane tracks for the busy executive officer. The Caine is sent as escort for a convoy of fueling ships to rendezvous with the third fleet. On the night of December 16, the Caine begins to roll. Queeg asks Willie why he has taken over the important job of tracking hurricanes. Queeg thinks Willie has made a mistake, because Willie's chart is completely bare of plots between Ulithi and the Philippines, and it was typhoon season. He orders Willie to go and doublecheck the storm information. The search yields no mistakes in Willie's calculations. Willie is nodding off in his bunk when the radioman brings him a storm warning. Maryk plots the location of the disturbance as just over three hundred miles South of the ship. The captain is suspicious that the message coincided with Willie's search for lost storm warnings.
The next morning the sea is worse still, and Queeg grows nervous. With the third fleet in sight, the ships attempt to refuel despite the terrible sea. Willie and Maryk watch as a ship tries and fails to fuel from the New Jersey. The third fleet is committed to providing air cover for General MacArthur's land invasion of the Philippines, so despite the danger, the fueling attempts continue. Finally, at half past one, the task force discontinues the attempt and begins maneuvering to avoid the storm, fleeing to the southwest.
Willie sleeps after his shift ends. He is awakened by the sound of crashing dishes and opens his eyes to find the ship tilted steeply to starboard. Willie scrambles up to the bridge, where he learns that the fleet was ordered to refuel again. Some of the ships had less than ten percent of their fuel remaining, and so could not weather the storm. Willie hears Queeg screeching rudder and engine orders to the helmsman. Queeg struggles to keep the ship pointed north into the wind, against the pressure of the wind and waves, but in accordance with the refueling orders. Downstairs, Willie finds Whittaker fretting that a hot lunch will be impossible to serve. Willie takes comfort in the fact that even in the extremity of the situation, the Navy functions as usual.
Willie reassumes the watch as the Caine attempts to steam southward in order to escape the storm. Queeg goes to the radar hut and leaves Maryk to execute the maneuver. The rudder is useless due to the current of the water, but Maryk finally accomplishes the order. When Queeg returns, Maryk suggests ballasting the water tanks so that the ship will ride lower in the water, making it less subject to the wind. Queeg refuses because having salt water in the tanks will cause a hassle later. Maryk also suggests disarming the depth charges to prohibit a major roll from knocking them free and endangering the ship. After arguing, Queeg finally concedes to this point, but then learns that Stilwell had already secured the charges because of standing orders from Keefer to do so whenever the ship was in danger. Queeg has Stilwell removed from the bridge and put on report for his insubordination, swearing to deal with him later.
The wind catches an exposed angle of the ship and tries to blow the ship back around into the waves. A gigantic wave breaks over the Caine, and the ship does not right itself. Maryk screams for the captain to try reversing the starboard engine, but at first Queeg just clings the telegraph, frozen. Queeg looks at Maryk with terror, but then reverses the starboard engine. Maryk begins issuing rudder commands without waiting for the approval of the captain. He sends Willie to the radar hut to check for the rest of the formation and orders the rest of the bridge staff back to their feet to resume battle stations. In the radar hut, Willie finds the crew faithless, scared, and ready to abandon ship. He does his best to restore their morale. Though the radar is completely dead, he orders them to resume checking it in order to give them something to do and ease their terror.