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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.”

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 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.