In preparation for an experiment, the crew evacuates the seaQuest, leaving only Commander Ford, Lt. Commander Hitchcock, Lieutenant Krieg, Chief Crocker, and Lucas aboard.

However, environmental extremists use the seaQuest's vulnerable state to seize control of the boat.

Dr. Raleigh Young's magma buoy launched from the seaQuest months earlier rockets out of the sea and crash lands onto an island.

A group of treasure hunters believe that the UEO is on their way to steal the fortune they hope to find.

Lucas and Lt. Commander Hitchcock enter the seaQuest in a competition to design a revolutionary new kind of single-seat submersible.

However, while testing it, Lucas is fired upon and the sub is captured by a rival developer.

While visiting Dr. Westphalen is visiting Malcolm Lansdowne, the two of them are captured by ousted dictator and escaped UEO prisoner Milos Tezlov, who wants Malcolm's dolphins to train for militaristic purposes.

However, when Kristin notices Tezlov's autistic son Caesar taking an extreme liking to dolphins, she forges a deal for her release, granting Tezlov passage aboard the seaQuest.