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

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.

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.”

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.

When Henderson is captured by Macronesia and sentenced to death, Hudson leads an undercover team to free her from the secure facility.

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.

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.

When Bridger is hurled across his quarters by an unknown force, it leads the seaQuest to find a hundred-year-old sunken ship. The spirits of those who perished there haunt its ancient hull, one of which possesses Dr. Westphalen.

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.

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.

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 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.

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

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.

Lucas oversees the maiden journey of a revolutionary new underwater train, while Ford and Henderson go on a secret date as passengers.

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.

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.

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.

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.

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.

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.

When the seaQuest visits the Broken Ridge mining colony, one of the colonists desperately pleads for the crew's help to escape from a dangerous situation straight out of the Old West.

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.