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.

A rogue nuclear physicist known only as the Marauder is determined to destroy the seaQuest.

As part of his plan, he rescues a revenge-minded dagger who was imprisoned by Bridger.

The seaQuest attempts to find out the cause of the disappearance of a number of haulers from one of the remotest colonies in the Free Zone where Hudson meets up with a person from his past.

When Henderson is captured by Macronesia and sentenced to death, Hudson leads an undercover team to free her from the secure facility.

After faking his own death a second time, radical environmentalist, Max Scully, returns and is pardoned for his murderous crimes.

Captain Hudson is ordered to escort him to an undersea ecological utopia, unaware of Scully's true intentions.