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.