The 21st century: mankind has colonized the last unexplored region on Earth; the ocean. But with newfound potential comes old-fashioned conflict and the United Earth Oceans Organization (U.E.O.) assigns the submarine, seaQuest DSV to keep the underwater peace and patrol the planet's final frontier. The captain of the seaQuest and its crew are its guardians, for beneath the surface lies the future.
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.
When Commander Ford and other crew members are contaminated with a deadly virus from a downed space station, Captain Bridger finds himself fighting against the clock and a government cover-up to save them.
An experimental submarine escapes from its moorings and manages to launch its nuclear weapons targeted at New Cape Quest, a city with 5 million inhabitants including relatives of the seaQuest crew.
Ford discovers an ancient warrior's helmet and sword that prove that the lost continent of Atlantis did exist. But the helmet may carry a deadly curse that could destroy Bridger and the crew.
On the mainland, Lucas falls for a beautiful woman and asks to resign from his position, however plans change when she is suddenly kidnapped by terrorists in an attempt to take control of seaQuest.
In order to gain control of seaQuest's nuclear weapons, a powerful psychic plants a nightmare in both Piccolo and Dagwood's minds, so that he will be invited on board to interpret their dreams.
The seaQuest is captured by an alien spacecraft and taken to Hyperion, a completely aquatic planet. The crew is then drawn into the civil war between the KrayTaks and the Hyperion resistance.
The crew members travel through a ""space-time sphere"" that rockets them back in time to October 1962 and places them in the midst of the Cuban missile crisis, where they have to try to prevent a nuclear holocaust.
The crew of seaQuest are joined by a reluctant Captain Nathan Bridger and set off to investigate a distress call from an underwater colony, only to find it is a trap by a renegade sub under the command of Captain Marilyn Stark, who has a personal vendetta against the seaQuest.
The crew protects a group of researchers at an abandoned mining outpost while they study an ancient chest found buried deep in the Mediterranean. However the chest proves to be like Pandora's box, housing a demon who escapes and then preys upon the landing party.
When Krieg brings back what he believes is a priceless gem, greed runs amok on the seaQuest. No one listens to his stories of sea monsters in the area, until one attacks the seaQuest.
seaQuest is hurriedly dispatched to rescue a crew returning from a manned mission to Mars when their space capsule crash lands in the Atlantic Ocean, but the president of an militarised Asian federation wants them too for his own reasons.
Wendy employs her psychic abilities and risks her life in a battle of the mind against Avatar, a powerful paranormal being who threatens the world's security with his ability to place political leaders into comas.
The crew transports a pop star to an island military base. Upon arrival they encounter an apparition of the Greek god Neptune, who mistakenly believes the singer and Henderson are actually Minvera and Medusa.
Captain Hudson is ordered to blow up an iceberg that has been directed towards Saudi Arabia by a corrupt businessman, only to find a group of refugees placed on the iceberg to prevent its destruction.
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.