Realizing that the ship needed a captain that had not been "sitting with his finger on the trigger", the new United Earth Oceans Organization (or UEO) recruits Bridger to assume command of the boat he designed.
But, when a renegade pirate submarine begins to endanger lives, Bridger can't help but be swept up in the life he tried to escape, especially when the captain of the rebel sub turns out to be the recently fired Stark on a revenge mission to destroy the seaQuest.
When the seaQuest visits the Broken Ridge mining colony, one of the colonists desperately pleads for the crew's help to escape from a dangerous situation straight out of the Old West.
Meanwhile, Lucas sneaks away to a party where Julianna and he may go “all the way.” The seaQuest is tricked into torpedoing a ship carrying dozens of child refugees, led by Cynthia Westphalen, Kristin's daughter.
However, when the Earth's crust begins to crack open underneath his father's power plant, the world is threatened by an unstoppable rise in ocean temperature which will melt the polar caps.
The crew of the new seaQuest shove off from New Cape Quest, Florida, but their shakedown cruise is interrupted when Genetically Engineered Life Forms (G.E.L.F.s) revolt and seize control of their island colony as well as a defensive weapons space base and threaten to destroy the Human race.
When a comet splashes into the water near seaQuest's location, it mysteriously disintegrates into particles, which cocoons the boat and impregnates it with an aggressive alien predator that disables the ship and attacks the crew.
When his airplane crashes in the South American jungle, Piccolo is kidnapped by a ruthless dictator from a militant confederation who has been secretly creating cloaked artificial life-forms that have gone out of control.
After receiving a plea for help from Commander Keller, a massive alien starship draws seaQuest from the water and takes the crew billions of light-years away to the far distant world of Hyberion where they are dropped in the middle of a civil war that threatens to destroy the boat and all aboard.
To prevent Hudson from destroying the iceberg, Deon plants Macronesian refugees on its surface, led by a former member of seaQuest's crew: Lieutenant Benjamin Krieg.
Special guest star: John D'Aquino After rescuing a group of children from a Macronesian attack, Henderson is captured and sentenced to death by President Alexander Bourne.
Upon discovering a viral outbreak caused by a rescue mission mounted by the original seaQuest over a decade earlier, Lucas develops a method to counteract the agent.