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.

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.

When genetically engineered people, no longer happy with their captivity, stage a revolt, seaQuest, with some new faces are called in to help.

When genetically engineered people, no longer happy with their captivity, stage a revolt, seaQuest, with some new faces are called in to help.

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.