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

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.

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.

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.

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.

A brand new power plant which is set to supply energy to the whole world goes wrong and there is a danger of the polar ice caps melting. Bridger decides he must sacrifice the seaQuest in order to save the world. Meanwhile, Lucas has a reunion of sorts with his father.

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.

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.

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

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.

Lucas and Lt. Commander Hitchcock enter the seaQuest in a competition to design a revolutionary new kind of single-seat submersible. However, while testing it, Lucas is fired upon and the sub is captured by a rival developer.

A blind astrophysicist and a NASA commander team up with the crew to battle a hostile alien, hidden in a fallen comet that seaQuest was attempting to recover.

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.

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.

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.

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.

The crew transports a pop star to an island military base. Upon arrival they encounter an apparition of the Greek god Neptune, who mistakenly believes the singer and Henderson are actually Minvera and Medusa.

A massive prehistoric crocodile is released from its icy tomb when extensive undersea farming and mining cause the temperature of the South Atlantic to rise.

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.

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.

Piccolo's estranged father seeks his help after his wife becomes addicted to an experimental drug. When Bridger and Smith are discovered in an embrace, rumours spread like wildfire about their supposed shipboard romance.