The crew of the the newly rebuilt SeaQuest must deal with a hostage crisis at a UEO prison colony, where genetically engineered soldiers have risen up against their captors.

The engineers of the alien spacecraft that the original seaQuest discovered before her destruction receive the message sent by the crew and relay their intentions, through Darwin, to make first contact with the Human race. While the crew are ecstatic, General Thomas and a hot-shot UEO lieutenant can only see things from a military perspective.

Seaquest gets called to a normally peaceful colony that is now experiencing mass hysteria and violence. Once Seaquest arrives, the same thing starts happening to the crew.

A budding romance starts between the doctor and the captain, as well as O'Neill and Henderson. While on shore leave, Piccolo has some family troubles with his parents.

Seaquest travels through an underwater black hole to 200 years in the future. Once there they discover a super computer who created the black hole to bring them to the future to help save the last two people on earth.

A malfunctioning A.I. sub begins firing on civilian targets. Seaquest is sent to track it down and destroy it. During the fight it is determined that the sub is using Captain Bridger's mental profile for its A.I. logic.

Seaquest receives a mayday from an underwater agricultural station. Upon arrival they find the station empty of the crew. Once back on board the flowers Henderson picked suddenly grow and begin attacking the ship.

Brody's Mom, who has been in cryofreeze for years, emerges and is targeted by someone trying to kill her for a crime she witnessed in the past.

Dagwood is accused and convicted of murder, but it's a case of mistaken identity.

One of the launches receives a distress call while returning to Seaquest. While responding to the call the launch is sucked into an underwater cave where they find another scientist who has been trapped for days.

A massive prehistoric crocodile is released from its icy tomb when extensive undersea farming and mining cause the temperature of the South Atlantic to rise.

The Seaquest finds an ancient helmet which seems to be from the lost city of Atlantis. A professor arrives to debunk this theory. However, the helmet starts warping the minds of the captain and some of his men.

Lucas falls head over heals for a woman he meets at a bar, but it turns out she has nefarious plans to use Lucas. She is only using Lucas to help her father take control of the Seaquest.

Seaquest tracks a comet that crashes into the ocean. The comet sinks but an alien life force emerges and begins to engulf Seaquest. Eventually the alien takes over one of the crew and begins searching for another of its kind.

A rogue psychic with tremendous powers targets UEO officials. Eventually all psychics are rounded up and placed in concentration camps. Wendy who is the only hope of stopping the psychic is also targeted by both the psychic and the UEO.

While en-route to a USO concert with a singer on board the crew encounters some strange mythological spirits. Once they arrive at the island, they discover it to be a very large pyramid. Within the pyramid they find the spirit of Neptune.

The Seaquest is called to an underwater research station that has discovered an ancient mysterious ark. Once the ark is opened an evil spirit is released which begins to infect and attack the researchers.

Dagwood and Piccolo have a strange shared dream, but the dream is only a means to an end for an evil psychic who wants to board Seaquest and steal some material.

Seaquest is transported to another planet after responding to a message from Commander Scott Keller. Once there they get involved with a civil war and a possible fight to the finish.

Piccolo's ex-cell-mate lures Tony into an escape plan. During the botched escape they crash into the jungle where an experimental cloaking warrior attacks them and the rescue crew sent from Seaquest.