An emotional time is at hand as the seaQuest's tour of duty comes to an end; Chief Crocker faces his retirement and the end of his marriage, Commanders Ford and Hitchcock are offered the same command, and Captain Bridger and Dr. Westphalen begin a romantic relationship. Most emotional of all is Lucas who realizes that his father is hardly a part of his life anymore. 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. With lava seeping into the sea, Bridger must sacrifice the seaQuest in order to save the world.
- As the crew takes a well earned time off, many considering other career choices or facing disappointments at home, Lucas struggles with being ignored by his parents again and Nathan and Stephanie finally explore a relationship beyond the captain and medical officer. Admiral Noyce contacts Seaquest when the power grid fails and the last communiqué from an underwater turbine farm, headed by Lucas' father, Dr. Wolnczak, that experienced a sea floor eruption, suggests that everyone has died. The underwater river of lava, two miles wide, causes increased water temperature, with the potential of melting the polar caps. SeaQuest tries to reach the power plant, but the unstable ocean vents erupt striking the hull and they are forced to abandon ship. Chief Crocker, having received a Dear John video letter from his wife, decides to risk a chance at saving any survivors of the underwater power plant. Only three make it, Dr. Wolenczk being one. To solve the lava flow problem, Nathan chooses to use the 100 megaton nuclear weapons aboard SeaQuest by driving it into the river and detonating remotely. Nathan Bridger puts his own life at risk when the auto pilot of SeaQuest fails and he must send the others to safety while he alone drives it into the open lava. A new SeaQuest must be built to replace it.