Ten years after its mysterious disappearance, the seaQuest appears back on Earth. A tough Navy officer, who had been obsessed with searching for the submarine, assumes command of the seaQuest due to the new hostile world climate.

Captain Hudson is ordered to blow up an iceberg that has been directed towards Saudi Arabia by a corrupt businessman, only to find a group of refugees placed on the iceberg to prevent its destruction.

The seaQuest attempts to find out the cause of the disappearance of a number of haulers from one of the remotest colonies in the Free Zone where Hudson meets up with a person from his past.

Lucas oversees the maiden journey of a revolutionary new underwater train, while Ford and Henderson go on a secret date as passengers.

Hudson must relieve his old commanding officer from duty onboard a heavily armed underwater base after the base fires on Macronesia.

When Henderson is captured by Macronesia and sentenced to death, Hudson leads an undercover team to free her from the secure facility.

Lucas must face up to Bridger over his potentially risky solution to combat an organism that threatens to reach epidemic proportions.

After faking his own death a second time, radical environmentalist, Max Scully, returns and is pardoned for his murderous crimes. Captain Hudson is ordered to escort him to an undersea ecological utopia, unaware of Scully's true intentions.

Captain Bridger seeks seaQuest's help to go deep into Macronesian waters and retrieve some top secret data crystals that reveal unspeakable atrocities committed against humanity 20 years earlier. The crimes in which Bridger and Ford may have been involved.

The crew members travel through a ""space-time sphere"" that rockets them back in time to October 1962. This places them in the midst of the Cuban missile crisis where they have to try to prevent a nuclear holocaust.

As the world leaders debate the renewal of the UEO charter a number of assassination attempts are made against the delegates.

SeaQuest docks at a penal colony where the prisoners are enslaved. Henderson recognizes one and inadvertently causes a riot allowing the inmates to escape and take hostages.

The seaQuest is drawn into the dangerous neutral area where the UEO and Macronesian borders meet the territory of a silent and elusive Asian power.