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.
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.
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.
O'Neill, unhappy with his work decides to resign and devotes himself to painting. Mariah, the dagger who led the uprising, is approached by a man who wants her to do something. And what she does is come on to O'Neill and makes him give her information about the SeaQuest.