The crew of seaQuest are joined by a reluctant Captain Nathan Bridger and set off to investigate a distress call from an underwater colony, only to find it is a trap by a renegade sub under the command of Captain Marilyn Stark, who has a personal vendetta against the seaQuest. They are attacked and find themselves defenceless and are forced to dive the ship and hide.
Darwin falls ill and will die if no cure is found, but a visiting scientist on an important UEO project is unconcerned with the fate of a single dolphin.
When a preserved annexe of the Great Library of Alexandria is discovered, many nations send their fleets to lay claim to its treasures. The UEO orders Bridger to mediate the dispute and sends a team of ESP parapsychologists to help the negotiations.
The crew of seaQuest rescue a warden and his only prisoner from beneath the ice cap. The prisoner escapes and reveals that he holds a deadly toxin which will be released unless the crew does as he says, which is launching the seaQuest's missiles against the UEO.
When Krieg brings back what he believes is a priceless gem, greed runs amok on the seaQuest. No one listens to his stories of sea monsters in the area, until one attacks the seaQuest.
The seaQuest discovers a group of children living in an old munitions facility on the sea floor and they must evacuate them, before, the structure collapses and unleashes a deadly explosion. Meanwhile, Lucas develops a crush on the teenage girl.
When Commander Ford and other crew members are contaminated with a deadly virus from a downed space station, Captain Bridger finds himself fighting against the clock and a government cover-up to save them.
When a small team from seaQuest board a ancient sunken ship in order to determine why it went down, they find themselves trapped in a series of very bizarre and supernatural events.
A hurricane threatens to prevent the rescue of a French sightseeing submarine which is stuck in a freshwater sink hole and running out of oxygen. When a team from the seaQuest are forced to the surface they must rely on each other to survive the storm.
When a vital component of seaQuest's air conditioning fails and regular channels fail, Krieg relies on a black market source called The Regulator. When Darwin disappears the seaQuest must track down the renegade who is seeking the meaning of life.
Hitchcock goes into an underwater gold mining colony in order to investigate a distress signal and discovers that the original and rightful owner of the mine and his family are being held hostage by an outlaw and his thugs.
When Lucas visits a communications base populated by a group of young computer experts, a famous computer hacker, who now runs the Node, persuades Lucas to break into the World Bank and divert funds for humanitarian causes.
seaQuest is hurriedly dispatched to rescue a crew returning from a manned mission to Mars when their space capsule crash lands in the Atlantic Ocean, but the president of an militarised Asian federation wants them too for his own reasons.
While in the middle of an special experiment when only a skeleton crew is aboard, seaQuest is boarded by a group of commandos who are quickly able to take control of the ship.
When a top-secret UEO project shows the approach of a catastrophic volcanic eruption, the crew of seaQuest must convince treasure seekers on the island to abandon their lifelong search or face certain death.
A renegade sub is sinking whaling ships, which are in themselves illegal and against their moral judgement, the crew of seaQuest must stop the sub from its mission. Meanwhile, Krieg is on a mission of his own: to have a cheeseburger, despite red meat being outlawed.
In the lead up to an important demonstration, Lucas is knocked unconscious and the Stinger, seaQuest's prototype high speed sub, is stolen.
A Servo-Croat dictator takes Drs. Westphalen and Lansdowne hostage in order to gain entrance into seaQuest in the hopes of using the ship's technology to rehabilitate his autistic son.
At a summit conference, Lucas and group of UEO leaders are taken hostage, leaving the seaQuest crew to uncover a mysterious and complicated plot whilst searching for the hostages.
Ford accidentally stumbles onto a colony of genetically altered humans, adapted by a scientist to live underwater.
Things threaten to go terribly wrong when the seaQuest crew discovers a million-year old spaceship. Their only hope is Darwin being the key to bridging the communications gap.
When the crew of seaQuest are tricked into torpedoing a refugee ship containing Westphalen's daughter, Dr. Westphalen, Ford, and Shan are trapped trying to save her.
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.
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. But the helmet 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.
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.
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.
Hudson must relieve his old commanding officer from duty onboard a heavily armed underwater base after the base fires on Macronesia.
As the world leaders debate the renewal of the UEO charter a number of assassination attempts are made against the delegates.
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 enviromentalist, Max Scully, returns and is pardoned for his murderous crimes, and 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 -- crimes in which Bridger and Ford may have been involved.
The crew members travel through a ""space-time sphere"" that rockets them back in time to October 1962 and places them in the midst of the Cuban missile crisis, where they have to try to prevent a nuclear holocaust.
When 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.
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.
