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.

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.

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 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.

An experimental submarine escapes from its moorings and manages to launch its nuclear weapons targeted at New Cape Quest, a city with 5 million inhabitants including relatives of the seaQuest crew.