A malfunctioning cargo submarine crashes into the side of Seamount and its damaged nuclear reactor threatens Sealab, forcing an evacuation. The oceanauts race against time to prevent the sub's reactor from melting down, but complicating the situation is its commander, who has an acrimonious history with Captain Murphy.
When the level of shark activity skyrockets around Sealab, they call in a shark expert to try to learn the cause and ensure safety for the oceanauts.
Sally and Bobby take matters in their own hands to stop an aquarium from capturing two of every sea creature on the Seamount.
Sealab is damaged in a storm, causing a leak that threatens to flood the station. But repairs are complicated by a crew member suffering a sudden bout of "green fever," an uncontrollable longing to be on the surface and close to nature.
The aquanauts try to find a sunken space probe before time runs out, but it may have been swallowed by a basking shark. Meanwhile, the impatient representative of the aerospace company accuses the sound technician involved in the search of being a foreign agent.
A red tide engulfs Sealab, cutting down its oxygen supply. Meanwhile, Gail becomes attached to a lost, young dolphin she found and tries to train it to rescue divers.