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.

Hudson must relieve his old commanding officer from duty onboard a heavily armed underwater base after the base fires on Macronesia.

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.