Cruising below the surface, Seaview experiences strange electronic interference from an unknown source. At the Nelson Institute of Marine Research, Admiral Nelson receives a jumbled communication from Crane. The interference builds to an explosive force, destroying Seaview and all hands. Hours later, as Nelson waits from news of Seaview's status from search vessels, a large crate is brought into his office. Inside is Mr. Pem (from "A Time To Die"), swearing to be reformed and hoping for a chance to rebuild his time device for the betterment of mankind. As Nelson begins to escort Pem from his office, a message comes in with news of the sinking of Seaview. In his grief, Nelson accepts Pem's offer to help in exchange for the use of Seaview's power to create a new device. After whipping up a temporary time machine, Pem and Nelson are whisked to Seaview twenty-four hours before the blast.
A search is made for the bomb while Nelson allows Pem access to the lab. Before long, Pem recreates his time device and sends Seaview back to the time of the Revolutionary War. As Major General Benedict Arnold and Major John Andre are brought aboard, Nelson plays for time, allowing Crane to devise a plan of distraction. Nelson accompanies Pem and the others on an inspection of the missile room, where an attack will be launched, winning the war for the British. This change in the timeline will eventually make Pem the most powerful man in the 20th century.
Crane executes his plan, rocking the sub voilently, sending everyone off balance, and causing Pem to drop his time device. Chief Sharkey and Seaman Kowalski rush the missile room as a struggle for control begins. Sharkey scoops up the device and runs for the control room. Pem sneaks out before Crane and men arrive to capture Arnold and Andre. Pem reaches the Reactor Room with his makeshift time machine, ready to exact revenge, when Crane and Sharkey enter. After a brief fight, Pem is killed when he is thrown into the reactor by Sharkey. The two men from history are sent back to shore just before Nelson goes forward in time to find the bomb Pem had planted earlier. The clock running, Nelson races to the missile room and launches the lethal device from a torpedo tube moments before it detonates. The danger over, Nelson and Crane quietly discuss the fate of Pem's device.
"It'll have to be destroyed, of course," Nelson says. "I'm afraid the world's not quite ready for this yet."
And Seaview sails off into television history.