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.

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 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.

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 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.

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.

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.

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.

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?

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.”