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.

Commander Ford, Dr. Westphalen, Lucas and Lieutenant Krieg are trapped on the surface of the ocean as a hurricane rages above them. Meanwhile, suffering severe damage from a lightning strike, the seaQuest must desperately search for a sunken French submarine before its passengers, all children, run out of air.

A virus found on board a sunken space station infects the crew. As Bridger rushes to find the inventor of the pathogen, a warrior submarine from an opposing confederation arrives to cover up their crimes, even if it means the destruction of the seaQuest.

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.

Mass murderer Dr. Rubin Zellar is unwittingly taken aboard the seaQuest. Placing him in custody, Zellar is able to escape and informs Bridger that he's hidden a toxin frozen in ice somewhere aboard the ship... a toxin that is surely melting with each passing second.

As the seaQuest undergoes inspection, Lieutenant Benjamin Krieg has a close encounter with an unknown life form while in a seaCrab in the Tonga Trench. When the creature lets him go, Krieg discovers a treasure trove of mysterious glowing stones; stones that may mean big money. However, is the bigger threat to seaQuest the greed that overtakes the crew or the unknown life form?

The seaQuest is ordered to entomb a munitions depot thought to be abandoned. However, when the crew discovers children living inside, Bridger must convince them to follow him to safety.

While investigating a black smoker, Darwin becomes seriously ill. Bridger must contemplate setting his long-time aquatic pal free in order to save his life.

The seaQuest discovers the lost Library of Alexandria sunken beneath the sea. However, when surrounding nations cannot agree on a peaceful way to share the discovery, Bridger must act as mediator before escalating tensions result in the destruction of the library.

Feeling isolated, unwanted, and unappreciated aboard the seaQuest, Lucas visits Node Three, a communications colony populated by other teenage computer geniuses. Node Three is led by legendary computer hacker Martin Clemens, aka. "Mycroft". However, Lucas soon finds himself caught up in the group's tampering with global finances and tampering's that have more motive than they appear.

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.

The first manned mission to Mars returns home to Earth, led by Commander Scott Keller, an old friend of Bridger's. However, a malfunction during re-entry plunges the capsule into the ocean where a corrupt general from a foreign confederation races to recover the astronauts before the seaQuest can.

In preparation for an experiment, the crew evacuates the seaQuest, leaving only Commander Ford, Lt. Commander Hitchcock, Lieutenant Krieg, Chief Crocker, and Lucas aboard. However, environmental extremists use the seaQuest's vulnerable state to seize control of the boat.

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

When an environmental radical begins to sink whaling ships, the UEO orders Bridger to find the attacker and destroy him. However, Bridger refuses on moral grounds and resigns as captain of the seaQuest.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

While visiting Dr. Westphalen is visiting Malcolm Lansdowne, the two of them are captured by ousted dictator and escaped UEO prisoner Milos Tezlov, who wants Malcolm's dolphins to train for militaristic purposes. However, when Kristin notices Tezlov's autistic son Caesar taking an extreme liking to dolphins, she forges a deal for her release, granting Tezlov passage aboard the seaQuest.

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.

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.

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.

When Commander Ford believes he saw a mermaid at the bottom of the ocean, Captain Bridger orders him to take shore leave. While on leave, Ford encounters the same woman again and soon finds himself ensnared in a mysterious scientist's unnatural experiment. Meanwhile, Lucas sneaks away to a party where Julianna and he may go “all the way.”

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.

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.