After the crew of the Seaview learns about disappearing nuclear missiles, Admiral Nelson and Captain Crane set off in the flying sub to investigate. While flying, they encounter an enemy submarine (which they ascertain is responsible for the missing missile) and they are shot down by it. The Admiral and Crane become separated after the flying sub crashes; the Admiral being found by a U.S. destroyer and Captain Crane being found and captured by the enemy submarine. Captain Crane learns that the captain of the enemy sub, Captain Ruiz, is stealing nuclear missiles for his country so it can gain more power.