Pirates rescued from a life raft hijack a freighter and force the crew to take them to a deep sea mining operation where they steal a shipload of valuable uranium ore. Captain Fathom and his crew are ordered to recapture the vessel, free the crew and return the ore before it winds up in the hands of an unfriendly nation.
When the captain of several freighters who have wrecked on a treacherous reef report they swerved to avoid being rammed by a ghost ship, Captain Fathom and his crew are asked to investigate. When the salvage operator responsible for causing the wrecks discovers Fathom's presence, he determines to destroy the adventurer, his ship and crew with torpedoes and magnetic mines.
Captain Fathom and the crew of the Argonaut are ordered to attend the signing of a peace treaty between two small peaceful island nations. When the chief of one of the islands accidentally sinks a boat belonging to the other archipelago, the peace treaty is off and war is on unless Fathom and his crew can avert disaster.