The overarching conflict is reminiscent of Moby-Dick: a powerful oil baron, known to the main characters only as a cyborg called "The Machine" until the final episodes, loses his arm and part of his face to Willy while committing an environmental atrocity and wants revenge upon "that rotten whale... and his boy".

Jesse and Randolph work with Mr. Naugle, the head biologist, and Marlene, a research assistant, who are studying Einstein, a dolphin, and Lucille, a sea lion, teaching them behavioral communication with normal humans.

The main villain of the series, similar in personality to Captain Ahab, is a cyborg called "The Machine" who holds Willy responsible for his loss of an arm and part of his face.

When not using his new submarine to create environmental havoc, he dons a mask and glove (perhaps a nod to the contributions of Michael Jackson to the films) for disguise and continues to run an oil company under his former identity, Rockland Stone.

They mainly function as comic relief; they are somewhat reluctant to carry out instructions to pollute and destroy the environment, preferring to slouch around and entertain themselves, and often making costly and catastrophic errors for The Machine.

Throughout the series, Jesse is constantly fighting plots and schemes hatched by The Machine to destroy Willy, such as releasing deadly parasites and creating genetic engineering giant squid predatory to orca, and to despoil the ecosystem, such as wanton spilling of garbage, toxic waste and oil into the sea.

Upon returning to Misty Island, Jesse and Willy become entwined in a Christmastime plot ("Yuletide or Redtide") (also series finale) to use a biodegradable jet ski (assumed to be a gift from his parents, Glen and Annie, but actually from Stone) for the release of deadly red tide to thrive in the unseasonably warm water, implied to be an effect of climate change.

When The Machine is defeated by teamwork and a sudden cold spell, saving everyone's good cheer, the Amphonids make themselves into a distorted Christmas tree and actually sing along with the townspeople, to their master's chagrin.