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.

When the air conditioning breaks down in the crew quarters, Krieg has no choice but to turn to "The Regulator".

He's a cut-throat black market trader who hides a shamed past with whom Bridger is familiar with and whom Lucas finds he can sympathize with.

In preparation for an experiment, the crew evacuates the seaQuest, leaving only Commander Ford, Lt. Commander Hitchcock, Lieutenant Krieg, Chief Crocker, and Lucas aboard.

However, environmental extremists use the seaQuest's vulnerable state to seize control of the boat.

Dr. Raleigh Young's magma buoy launched from the seaQuest months earlier rockets out of the sea and crash lands onto an island.

A group of treasure hunters believe that the UEO is on their way to steal the fortune they hope to find.

Lucas and Lt. Commander Hitchcock enter the seaQuest in a competition to design a revolutionary new kind of single-seat submersible.

However, while testing it, Lucas is fired upon and the sub is captured by a rival developer.

A brand new power plant which is set to supply energy to the whole world goes wrong and there is a danger of the polar ice caps melting.

Bridger decides he must sacrifice the seaQuest in order to save the world. Meanwhile, Lucas has a reunion of sorts with his father.

Piccolo's estranged father seeks his help after his wife becomes addicted to an experimental drug.

When Bridger and Smith are discovered in an embrace, rumours spread like wildfire about their supposed shipboard romance.

Ford discovers an ancient warrior's helmet and sword that prove that the lost continent of Atlantis did exist.

The helmet though may carry a deadly curse that could destroy Bridger and the crew.

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.