Extra-terrestrials that are searching for the beginnings of intelligent life are welcomed aboard seaQuest, only to be taken captive by a general determined to have their advanced technological secrets.

An experimental submarine escapes from its moorings and manages to launch its nuclear weapons targeted at New Cape Quest, a city with 5 million inhabitants including relatives of the seaQuest crew.

Ford discovers an ancient warrior's helmet and sword that prove that the lost continent of Atlantis did exist.

The helmet though may carry a deadly curse that could destroy Bridger and the crew.

A rogue nuclear physicist known only as the Marauder is determined to destroy the seaQuest.

As part of his plan, he rescues a revenge-minded dagger who was imprisoned by Bridger.

When his plane crashes in the South American jungle, Piccolo is kidnapped by a ruthless dictator who he finds out has secretly been creating artificial life forms that have now gone out of control.

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.

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.

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

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.