Captain Murphy is horrified to discover that his beloved HappyCake Oven? ("Makes real cupcakes!") is missing from Sealab. He orders the reluctant crew to search for it in a submersible, and they are attacked by a mutated-giant-killer squid. Meanwhile, Sparks continues his fiendish quest for world domination.

A news item about Django, the little monkey whose brain was transplanted into a robot-body, plunges the crew into a lengthy debate on whether or not they would allow their brains to be put in robot-bodies. Meanwhile, Sealab is in imminent danger of imploding, and Dr. Quinn is the only one on board who seems to care.

Debbie decides that she wants to have a baby, and now. She interviews all of the male crew members to see who would make the best father for her child. The men, of course, turn it into a childish competition. In the meantime, Stormy almost learns a valuable lesson in race relations... but doesn't, quite.

A bloodthirsty, killer alien has boarded Sealab, and trapped the entire crew. His shimmering form is seemingly everywhere, rending flesh from human bones, as the remaining survivors cower on the bridge. Once again, it's up to the brave Dr. Quinn (with a little help from Old Gus and Dolphin Boy) to save the day.

After a huge explosion destroys Sealab, Stormy and Dr. Quinn are mysteriously transported fifteen minutes into the past, which puts them in a position to save Sealab from being destroyed in the first place. But Captain Murphy imprisons them, assuming they are doppelgangers. And so Sealab is destroyed by another huge explosion, which then transports another Stormy and Dr. Quinn fifteen minutes into the past, and so on, and so on...