When genetically engineered people, no longer happy with their captivity, stage a revolt, seaQuest, with some new faces are called in to help.

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.

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.

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.

In response to the voice of a child calling for help, the seaQuest journeys through an underwater vortex and find themselves 250 years in the future where humans are on the brink of extinction.

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.

A distress call from an underwater horticultural colony leads the crew into an investigation of the mysterious disappearance of all human life inside the former paradise.

When a woman is released from a cryogenic institute after 22 years, she is targeted by an assassin.

Brody attempts to help her, and discovers that she is linked to his past and to a possible murder.

Dagwood maintains his innocence after being found guilty of murdering the genetic engineer who created him, despite having apparently been caught in the act on video.

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.

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.

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.

On the mainland, Lucas falls for a beautiful woman and asks to resign from his position, however plans change when she is suddenly kidnapped by terrorists in an attempt to take control of seaQuest.

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.

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 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.

The crew protects a group of researchers at an abandoned mining outpost while they study an ancient chest found buried deep in the Mediterranean.

However the chest proves to be like Pandora's box, housing a demon who escapes and then preys upon the landing party.

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.

In order to gain control of seaQuest's nuclear weapons, a powerful psychic plants a nightmare in both Piccolo and Dagwood's minds, so that he will be invited on board to interpret their dreams.

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.

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.