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.
When a preserved annexe of the Great Library of Alexandria is discovered, many nations send their fleets to lay claim to its treasures. The UEO orders Bridger to mediate the dispute and sends a team of ESP parapsychologists to help the negotiations.
The crew of seaQuest rescue a warden and his only prisoner from beneath the ice cap. The prisoner escapes and reveals that he holds a deadly toxin which will be released unless the crew does as he says, which is launching the seaQuest's missiles against the UEO.
The Sea Quest crew is on its way to demolish an abandoned munitions plant. As they get closer they realize it isn't abandoned at all, there are six children trapped inside. One of the children is sick and needs to be transported to the ship right away, while the oldest boy is very hesitant to leave and runs off. Lucas is thrilled to have others his age on the boat and gets to show the oldest girl on a tour of the ship. Bridger must juggle keeping the two youngest boys out of his hair while trying to help Commander Ford get the last child out of the compound before it ...
The Captian and crew are at risk after being exposed to biological contamination that killed the crew of an underwater facility. Contamination came from a downed French space station called Liberte, found on the ocean floor.
When Bridger is hurled across his quarters by an unknown force, it leads the seaQuest to find a hundred-year-old sunken ship where the spirits of those who perished there haunt its ancient hull, one of which possesses Dr. Westphalen.
SeaQuest investigates an undersea mining facility after receiving a distress signal. Once they arrive, everything seems fine until they hear from one miner that it's not. The miner turns out to be the mine owner. The mine is not under UEO's jurisdiction, but they find they must help out even though doing so puts the crew in a dangerous situation.