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.

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.

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.

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.