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 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.