Bridger responds to a plea from an old girlfriend living in an underwater colony that has been dedicated to non-violence.

After ten years of peace, the citizens are trying to kill each other.

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.

Henderson, Lucas, Brody, and O'Neill are drawn into a furious underwater whirlpool that pulls their shuttle beneath the ocean floor and into a maze of ancient caverns.

Wendy employs her psychic abilities and risks her life in a battle of the mind against Avatar, a powerful paranormal being who threatens the world's security with his ability to place political leaders into comas.

The seaQuest is captured by an alien spacecraft and taken to Hyperion, a completely aquatic planet.

The crew is then drawn into the civil war between the KrayTaks and the Hyperion resistance.

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

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.