It’s been ten years since the seaQuest’s mysterious disappearance, but now the massive sub has been found in the middle of a wheat field. Then the old crew also start reappearing in different places.
A tough minded military officer, who had been assigned to figure out what happened to seaQuest, is put in charge of getting her back in the ocean, and then to commanding her and the new crew, as the boat is sorely needed in the current troubled times.
When Lucas is asked to help on the maiden voyage of an underwater hyper-speed tube train system, Ford and Henderson use the train’s maiden voyage to go on a secret romantic trip. However, the corporation in competition with the train plans to sabotage its maiden voyage, putting Lucas, Ford and Henderson’s life at risk, if they can’t foil the plot.
Lucas finds he is at odds with his former Captain, Nathan Bridger, when an ocean borne organism threatens to kill all ocean life. Lucas and Bridger differ on the correct solution to this world wide impending threat, and know that only one solution is the correct one. However, which solution is the correct one? Both strongly believe they have the correct answer which will save the world.
Max Scully returns and plans to use seaQuest's laser banks to destroy a stockpile of underwater nuclear weapons to destroy the human race, save for his environmental paradise, Ecotopia.
Bridger, Ford, Lucas, and Dagwood must infiltrate a Macronesian base, formerly controlled by the UEO, to locate top-secret data that link Bridger and Ford to crimes against humanity.
seaQuest is thrown back in time to 1962, where they find that all of mankind has been destroyed because of the Cuban Missile Crises. They must go further back in time to prevent the holocaust.