Horace L. Hunley launches his submarine, the H.L. Hunley, into Charleston Harbor, but the mission ends in tragedy as the craft sinks with all hands. To fulfill the blockade, General Beauregard has the ship raised and places Gen. Pierre G.T. Beauregard Donald Sutherland in charge, turning a grim accident into a renewed effort to strike at Union ships from the harbor's depths. He begins to assemble a crew, and after some difficulty, enough volunteers step forward to man the vessel, with the command ultimately resting on Lt. George Dixon. The men train, cranking the propeller and learning to synchronize their movements, while tensions simmer among them as personalities clash and old doubts simmer beneath the surface.
Dixon’s mind drifts back to the Battle of Shiloh, where a gold coin given to him by his wife—who would later perish in a steamboat explosion caused by a drifting mine—appears to have saved his life by deflecting a bullet. The crew lowers the Hunley, testing its silence and resilience as it sits on the bottom to gauge how long it can endure submerged pressure, nearly getting wedged in the dark. The U.S. Navy is alerted to the submarine’s existence, forcing the crew to consider every risk and contingency. They vote that if they become trapped after an attack, they will open the ballast valves and flood the submarine rather than risk suffocation, a decision that will weigh heavily on them in the hours to come.
The Hunley’s first mission is intended against the USS Wabash, but the attack does not go as planned and fails to deliver the decisive strike they seek. In response to evolving warnings, the ship is fitted with draped metal chain netting along its sides, a precaution meant to blunt the hull, while a loose line attached to the torpedo becomes tangled in the propeller, forcing a dangerous and delicate cut to free it as sailors aboard the Wabash fire upon the submerged craft. Beauregard then proposes a revised tactic: place the torpedo at the end of a long spar to reach targets more effectively. The Housatonic is ordered to shift position in the harbor and to keep moving so it cannot be entangled by netting, while Lt. Alexander is ordered to Mobile, Alabama, and a fresh volunteer earns a place on the crew.
On February 17, 1864, the CSS H. L. Hunley sails out again and closes with the USS Housatonic. The torpedo drives into the side of the Union ship, detonating with a blast that sinks the Housatonic—the first ship ever sunk by a submarine. A stray bullet from the submarine’s own craft fractures a window in the conning tower and wounds Dixon, while the explosion hollows the Hunley itself, opening seams and letting water flood the hull. With no way to release ballast or pump, the submarine sinks to the bottom, and, true to their vow, the crew floods the vessel and is lost. A memorial service in Charleston honors Beauregard and the Hunley crew, and, inside the wrecked submarine, Dixon catches a vision of his wife welcoming him into the hereafter.