A bureaucratic mix-up results in Hermes receiving a mandatory fishing license. The crew takes the Planet Express Ship to the center of the Atlantic Ocean, and starts fishing. After failing to catch anything, a bored Bender fashions a large fish hook made from Amy's beach umbrella, with Hermes' Manwich on it, and attaches it to the ship's unbreakable diamond filament tether.
Sunset comes, and the crew is ready to head back to New New York. Bender begins to haul in his line, but he has caught a colossal-mouth bass. The bass dives, dragging the ship to the bottom of the ocean before the hook slips loose. The Planet Express Ship survives its trek to the bottom, but its engines will not work underwater.
Professor Farnsworth conveniently has an anti-pressure suppository which Fry uses to go foraging for food with Bender and Dr. Zoidberg. Separated from them, Fry glimpses a mermaid; but when he returns to the ship, no one believes him. That night, the mermaid Umbriel lures Fry out of the ship, and they leave to explore the wonders of the ocean bottom. Meanwhile, Zoidberg finds a new home, a large conch shell.
The next morning, the crew finishes modifying the ship to return to the surface, but finds Fry missing. They set off following Zoidberg's sense of smell, and find the legendary lost city of Atlanta. There they find a civilization of merpeople with southern accents. A documentary (narrated by Donovan) explains that Atlanta moved offshore in an effort to boost tourism and become a bigger Delta hub. The city overdeveloped and its excess weight caused it to sink to the bottom. Everyone that stayed with the city evolved into merpeople, with the assistance of leaking caffeine from Atlanta's Coca-Cola plant.
Ready to leave, the crew heads back to the ship. Zoidberg announces he is staying (as usual, no one cares) but discovers his house has burnt down, after Bender left his cigar inside (Hermes notes the impossibility of this situation). Fry settles in to enjoy his life with Umbriel, but when he discovers that the Atlantans' evolution (the "mermaid problem") has made them unable to have sexual intercourse with humans, he runs to try to catch his friends. The ship leaves without him, but Bender's hook is still attached to the tether. Fry grabs hold and is dragged behind the ship. The colossal-mouth bass returns, and is hooked when it swallows Fry whole. The bass stays caught, and Fry returns to the surface with the rest of the crew. Bender's bass sets a world record, until Fry falls out of him and the weight is lowered; at which point Bender begins choking him. Dr. Zoidberg, having lost his under-sea home, reveals he now lives inside the bass.