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.

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.

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.

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 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.

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.

UEO Secretary General Andrea Dre travels aboard the seaQuest en route to a conference where she invites Lucas to join her to speak out on his work with Darwin. However, Lucas soon finds himself held hostage along with the leaders of the other UEO confederations.

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

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.

The seaQuest makes the biggest discovery in Human history when they discover an alien starship entombed in an undersea rock face; trapped there for over a million years. When an away team goes inside the ship, they find that they might not be the only thing aboard it.

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.

When the air conditioning breaks down in the crew quarters, Krieg has no choice but to turn to "The Regulator". He's a cut-throat black market trader who hides a shamed past with whom Bridger is familiar with and whom Lucas finds he can sympathize with.

Dr. Raleigh Young's magma buoy launched from the seaQuest months earlier rockets out of the sea and crash lands onto an island. A group of treasure hunters believe that the UEO is on their way to steal the fortune they hope to find.

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.

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.

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 Nathan Bridger is hauled out of retirement to command the new submarine SeaQuest, under the authority of the United Earth/Oceans Organization. His ship goes up against pirate forces commanded by Marilyn Stark, a former SeaQuest captain who tried to instigate a war.