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.

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.

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.

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.

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.

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.