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1st Season
1."To Be or Not to Be"
During a tense confrontation the current Captain of the seaQuest Marilyn Stark ignores the orders to stand down and continues preparations to fire on the opposing vessel. She is relieved of command by Comm. Jonathan Ford. Thirteen months later the seaQuest has been recommissioned to be a Scientific Exploration and Research Vessel. Now all that is needed is a new captain. Ex Navy Captain Nathan Bridger is recruited for the job against all his objections. Ford is asked, by Admiral Noyce, to be very cocky and headstrong so the Captain will want to take command of the seaQuest. Darwin is brought on board by Noyce as an incentive for Nathan to stay. In a tense moment when Ford falters, Bridger takes command. After the crisis has passed Ford fills him in on the actual situation. Bridger is not happy. A virus causes all the systems on the seaQuest to shut down, and Lucas must figure out how to work around it to get the boat up and running again. They find out that the virus was planted by Captain Stark. Bridger does finally take full command of the seaQuest, uniform and all, and with the help of Darwin is able to stop Stark's plan to destroy the seaQuest.
2."The Devil's Window"
Two miles beneath the surface, seaQuest explores one of the ocean's truly remarkable phenomena: steaming hot hydrothermal vents play host to an underwater forest of giant tube worms and other forms of life where none was thought possible. But when Darwin the dolphin becomes deathly ill, Captain Bridger is forced to choose between the mission at hand and the life of one of his crew.
3."Treasure of the Mind"
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.
4."Games"
The crew of seaQuest rescue a warden and his only prisoner Dr. Rubin Zeller from beneath the ice cap. The crew realizes that Dr. Zeller is posing as the warden and 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.
5."Treasures of the Tonga Trench"
Greed plays a powerful part in this episode. After a test dive Krieg brings back what he believes is a priceless gem. Everyone on board wants their shot at the treasure. No one listens to his stories of sea monsters in the area, until one attacks the seaQuest.
6."Brothers and Sisters"
The seaQuest discovers a group of children living in an old munitions depot on the sea floor. All of the children, save one, are brought on board. Commander Ford must convince a young man to leave his home and return to seaQuest with him because the structure is failing and could unleash a deadly explosion at any moment.
7."Give Me Liberte"
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.
8."Knight of Shadows"
When a small team from seaQuest board a ancient sunken ship in order to determine why it went down, they find themselves trapped in a series of very bizarre and supernatural events.
9."Bad Water"
A hurricane threatens to prevent the rescue of a French sightseeing submarine which is stuck in a freshwater sink hole and running out of oxygen. When a team comprised of Lucas, Dr. Westphalen, Krieg, and Comm. Ford are forced to the surface they must rely on each other to survive the storm.
10."The Regulator"
When a vital component of seaQuest's air conditioning fails and regular channels get them nowhere, Krieg relies on a black market source called The Regulator. When Darwin disappears the seaQuest must track down the renegade who is seeking the center of the universe.
11."seaWest"
Hitchcock goes into an underwater gold mining colony in order to investigate a distress signal and discovers that the original and rightful owner of the mine and his family are being held hostage by an outlaw and his thugs.
12."Photon Bullet"
Lucas is invited to stay for a time at NODE 3, a communications instillation. Since he feels under-appreciated onboard the seaQuest he accepts. But he gets more than he bargained for when he is asked to hack into the World Bank. He must choose between doing what's wrong and what's right.
13."Better Than Martains"
seaQuest is hurriedly dispatched to rescue a crew returning from a manned mission to Mars, which is captained by Bridger's friend Scott, when their space capsule crash lands in the Atlantic Ocean, but the a general of an militarised Asian federation wants them too for his own reasons.
14."Nothing But the Truth"
While in the middle of an special experiment when only a skeleton crew is aboard, seaQuest is boarded by a group of commandos who are quickly able to take control of the ship. Commander Ford must rescue those that are taken hostage, including Hitchcock and Lucas, and the clock is ticking.
15."Greed for a Pirate's Dream"
When a top-secret UEO project shows the approach of a catastrophic volcanic eruption, the crew of seaQuest must convince treasure seekers on the island to abandon their lifelong search or face certain death.
16."Whale Song"
A renegade sub is sinking whaling ships, which are in themselves illegal. Against their moral judgement, the crew of seaQuest must stop the sub from its mission.
17."The Stinger"
In the lead up to an important demonstration, Lucas is knocked unconscious and the Stinger, seaQuest's prototype high speed sub, is stolen. He and Hitchcock must scramble to get it back in time for the demonstration.
18."Hide and Seek"
A Servo-Croat dictator, played by William Shatner, takes Drs. Westphalen and Lansdowne hostage in order to gain entrance into seaQuest in the hopes of using the ship's technology to rehabilitate his autistic son.
19."The Last Lap at Luxury"
At a summit conference, Lucas and group of UEO leaders are taken hostage. The seaQuest crew discovers that Secretary Dre is a traitor. They must find Lucas and the others before the Secretary has them disposed of.
20."Abalon"
A scientist thought long dead has created a new world under the ocean filled with genetically altered humans. Having seen one of these people swimming around under the ocean unassisted, Ford thinks he's going crazy. When he disappears the crew must decide if they want to believe his stories of mer-people in order to find him.
21."Such Great Patience"
The seaQuest experiences an undersea earthquake and aftershock that reveals a huge alien spacecraft. Commander Scott Keller comes aboard to lead an exploratory team to the alien ship. Keller and the others come face to face with an alien. Genderless yet sophisticated in design, it moves gracefully with large eyes unblinking. It is apparent the alien wants to talk with Darwin and that they are not there for human contact. Their only hope is Darwin being the key to bridging the communications gap.
22."The Good Death"
When the crew of seaQuest are tricked into torpedoing a refugee ship containing Westphalen's daughter, Dr. Westphalen, Ford, and Shan are trapped trying to save her. Ortiz and one of the refugee's must try and rescue them, while steering clear of a paranoid dictator.
23."An Ocean on Fire"
A brand new power plant which is set to supply energy to the whole world by Lucas's father 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.
2nd Season
24."Daggers (1)"Events revolving around the period between the years 1997 and 2003, which has become known as the Dark Age of Genetics, where the beings created during this time are known simply as 'Daggers'. Daggers that have lived a sheltered life in a type of military camp decide that they want their freedom. Taking the military men on the island captive, they set their sites on the heads of the UEO.
25."Daggers (2)"The seaQuest and it's crew must stop Mariah from blowing up all of the oxygen regeneration plants around the world. They must prove to her that the Dagger baby onboard seaQuest needs as much oxygen as humans. Mariah must decide if they are telling the truth.
26."The Fear That Follows"After Bridger's invitation is accepted Extra-terrestrials that are searching for the beginnings of intelligent life are welcomed aboard seaQuest. They are very taken with Lucas and he must choose to go with them, or stay here on Earth.
27."Sympathy for the Deep"
Bridger responds to a plea from an old girlfriend living in an underwater colony that has been dedicated to non-violence. After ten years of peace, the citizens are trying to kill each other.
28."Vapors"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, rumors spread like wildfire about their supposed shipboard romance.
29."Playtime"In response to the voice of a child calling for help, the seaQuest journeys through an underwater vortex and find themselves 250 years in the future where humans are on the brink of extinction. They must find a way to get the two remaining people on Earth together, or they will never be able to return home. The past can't exist without the future.
30."The Sincerest Form of Flattery"
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.
31."By Any Other Name"
A distress call from an underwater horticultural colony leads the crew into an investigation of the mysterious disappearance of all human life inside the former paradise. When it is discovered, via Henderson bringing one of the plants on board, that it was the plants that killed the people the crew must figure out a way to kill these deadly plants.
32."When We Dead Awaken"
When a woman is released from a cryogenic institute after 22 years, she is targeted by an assassin. Brody attempts to help her, and discovers that she is his mother. It is found out that General Thomas is behind her assassination attempts, and Brody must rescue her before McGaff finishes what he started.
33."Special Delivery"
Dagwood maintains his innocence after being found guilty of murdering the genetic engineer who created him, despite having apparently been caught in the act on video.
34."Dead End"Henderson, Lucas, Brody, and O'Neill are drawn into a furious underwater whirlpool that pulls their shuttle beneath the ocean floor and into a maze of ancient caverns. Meeting up with a scientist, Marcus Rawlings, they must bang together a new submarine in order to escape the caverns. The plot thickens when it is found out that there is only enough air in the pod for 4 people. They must decide who will be left behind.
35."Meltdown"
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.
36."Lostland"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 Ortiz. Ford must over come his seeing a ghost and take command of seaQuest. Time is running out and they need to find a cure.
37."And Everything Nice"
On the mainland, Lucas falls for a beautiful woman and asks to resign from his position. But suddenly, she is kidnapped by terrorists in an attempt to take control of seaQuest
38."Dream Weaver"A blind astrophysicist, Tobias LaCont, and a NASA commander, Scott Keller, team up with the crew to battle a hostile alien, hidden in a fallen comet that seaQuest was attempting to recover. When the alien takes Henderson hostage they must find a way to save her.
39."Alone"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.
40."Watergate"The crew transports a pop star, Sara Tonin, to an island military base where she is to give a concert for the troops. Upon arrival they encounter an apparition of the Greek god Neptune, who mistakenly believes the singer and Henderson are actually Minvera and Medusa, and he wants them to come home, whether they want to or not.
41."Something in the Air"
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 a Pandora's box, housing a demon who escapes and then preys upon the landing party
42."Dagger Redux"
A rogue nuclear physicist known only as the Marauder is determined to destroy the seaQuest. As part of his plan, he rescues a revenge-minded dagger, Mariah, who was imprisoned by Bridger.
43."The Siamese Dream"
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.
44."Splashdown"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 must sacrifice themselves and their ship to destroy the KrayTaks before the KrayTaks destroy the small resistance on the other side of Hyperion.
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