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.
Maryk is still giving the commands, but he is checking with the captain for approval once again. Maryk again requests permission to ballast the tanks, but Queeg refuses again. A swell knocks the ship almost sideways, and Maryk asks permission to head the ship into the wind for safety. Queeg insists that command would order the turn if they thought it appropriate. The ship will not come around. A gigantic wave crashes over the Caine and the floor of the bridge fills with water. The Caine rolls over almost onto its side. Maryk barks engine orders, but Queeg, still clutching the telegraph, is too petrified to move. Finally, Maryk has to pry the controls from Queeg's hands. Maryk reverses the engines and the rudder, pointing the bow back into the wind and saving the ship.
They begin coming around, and Willie and the rest of the bridge recover from their shock. Maryk says they will ride out the storm for a half-hour or so until conditions improve. Queeg suddenly comes out of his stupor and contradicts Maryk's order. Maryk explains that heading into the wind was the only way to save the ship for the time being. Maryk and Queeg begin shouting contradictory orders. Maryk goes to the captain, salutes him, and says, "Captain, I'm sorry, sir, you're a sick man. I am temporarily relieving you of this ship, under Article 184 of Navy Regulations." Queeg continues issuing commands. As duty officer, the decision of what to do finally falls to Willie. Stilwell is begging for directions, and finally Willie affirms Maryk's orders.
Maryk, now officially in command, brings the ship around and immediately orders the ballast tanks filled. Queeg curses Maryk and threatens everyone with arrest for mutiny. Maryk orders Queeg to keep quiet or go to his cabin. Their arguing is interrupted by the appearance of a submerged ship's hull in the water. Survivors are spotted, and Maryk executes a quick rescue. As they continue circling and looking for survivors, the weather begins to lighten, and Queeg declares that he is reassuming command of the ship. Maryk orders Queeg to leave the bridge. The captain demands to stay.
Captain Queeg's inability to act rationally in dangerous circumstances finally becomes unbearable in the life-and-death situation of the typhoon. Maryk relieves Queeg for fear that allowing him to remain in command will doom the ship. Whether or not Maryk makes the correct decision is the question that consumes the next section of the novel. On one hand, Queeg was simply following the last orders that he received, steaming north and attempting to support the fleet in refueling for the attack on the Philippines. Though Maryk's decision appears inevitable, from one point of view, Queeg does nothing wrong. His insistence on steaming north is in compliance with his last known order from the fleet. Even Queeg's decision not to ballast the water tanks could be seen as a good choice. Queeg might have assumed that because the commandant in New Jersey was aware of the Caine's situation, it would have ordered the tanks ballasted and a new course into the wind had it thought that necessary. The question is one of faith in superiors. Should a ship, and the hundreds of people serving on it, live and die by what the Navy says, even if the orders are wrong? The novel hinges around that question. Maryk is not willing to die and let others die in observance of naval procedures, and takes his life into his own hands.
As soon as Maryk takes over, the contrast between his leadership and Queeg's is blinding. Maryk already has the respect and trust from the crew that Queeg never achieved, and Maryk's orders are carried out with faith and without hesitation. His knowledge of the sea and his calm demeanor have an immediate and unconscious effect on the crew, who come out of their corners and ease their grips on the pipes when he comes into command. Urban, who had been crying and screaming, "Oh God, Oh God," while Queeg attempted to pilot them through the storm, comes back to his senses and resumes his duty. Even Willie is mesmerized by Maryk, who strikes Willie as a "father, leader, and savior." Using his knowledge of the sea, Maryk successfully pilots the Caine through the remaining danger and even manages to rescue some survivors from a nearby capsized ship.
Maryk's example of what a captain should be to a crew also comes into contrast with what Keefer is. When the two officers go to turn Queeg in aboard the New Jersey, the difference between them reveals itself pointedly. Maryk is impulsive and always ready for action, whereas Keefer prefers analysis and gets frightened in the face of drastic action. Keefer gets cold feet when he sees the representation of the Navy's power aboard the New Jersey. When it comes down to it, Keefer is a coward and acts for the preservation of his own position, while Maryk is willing to go forward and risk his own neck so that the entire crew of the Caine will be safe. This willingness and selflessness of Maryk's is what saves them all in the typhoon.