Extra-terrestrials that are searching for the beginnings of intelligent life are welcomed aboard seaQuest, only to be taken captive by a general determined to have their advanced technological secrets.

When a woman is released from a cryogenic institute after 22 years, she is targeted by an assassin.

Brody attempts to help her, and discovers that she is linked to his past and to a possible murder.

A blind astrophysicist and a NASA commander team up with the crew to battle a hostile alien, hidden in a fallen comet that seaQuest was attempting to recover.

When his plane crashes in the South American jungle, Piccolo is kidnapped by a ruthless dictator who he finds out has secretly been creating artificial life forms that have now gone out of control.

Ten years after its mysterious disappearance, the seaQuest appears back on Earth.

A tough Navy officer, who had been obsessed with searching for the submarine, assumes command of the seaQuest due to the new hostile world climate.