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.

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.”

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.

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.

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.

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.

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.