At the dawn of the 20th century, British archaeologist Professor Aitken, Donald Bisset and his son Charles, Peter Gilmore, hire Captain Daniels, Shane Rimmer, and his ship the Texas Rose to voyage at sea with a bold goal: to test a diving bell engineered by Greg Collinson, Doug McClure, in the quest for proof of the fabled city of Atlantis.
On their first descent, Charles and Greg are assaulted by a reptilian sea monster that bursts through the bell’s hull. Greg uses a live wire to electrocute the creature, and the crew unearth a solid gold statue that seems to confirm Atlantis exists. Back on deck, the discovery triggers a mutiny as Grogan, Hal Galili and Fenn, John Ratzenberger, along with Jacko, Derry Power, plot to seize the treasure. The line to the diving bell is cut, trapping Greg and Charles at the seabed, while a shot from the mutineers fatally wounds the Professor.
A colossal octopus—the Sentinel—attacks, a creature sent by Atlantis’s inhabitants. The mutiny’s chaos leaves Greg, Charles, and the four crewmen captured; only Sandy, the ship’s cabin boy, and the professor remain free aboard the Texas Rose. They are hauled to a cavern beneath the ocean floor, where they meet Atmir, Michael Gothard, a member of Atlantis’s ruling class, and the spearl-wielding Guardians. Atmir promises safety and explains that Atlantis comprises seven cities; two have already sunk beneath the waves, and a third lies abandoned.
Their journey through a prehistoric swamp inhabited by the Mogdaan brings the group to the city of Vaar. Five of the surface-dwellers are imprisoned while Charles is taken to Chinqua, the royal city. Charles, a scientist by training, is granted an audience with King Atraxon, Daniel Massey, and Queen Atsil, Cyd Charisse, who reveal their plan to shape human history using mind powers and claim they originally came from Mars.
Meanwhile, Greg and the Texas Rose crew befriend Briggs, Robert Brown, the captain of the long-missing Mary Celeste, who has become the unofficial leader of the human slaves—among them his daughter Delphine, Lea Brodie. Briggs warns that the Atlanteans will grant them gills so they can never return to the surface, while they stand guard against the marauding Zaargs. A sudden Zaarg attack kills Briggs, and Delphine helps Greg and the others plan a rescue of Charles.
Charles grows fascinated by the Atlanteans’ utopia, but Greg arrives in time to snap him back to reality, and together they rescue the others from Atlantean influence. The escape route leads through the swamp where the Mogdaan claims Jacko’s life, and the party presses on toward the diving bell. Atmir and the Guardians confront them with telekinetic force, conjuring violent water eruptions to deter their flight, yet Delphine, whose gills keep her bound to Atlantis, bravely covers their retreat.
They reach the diving bell and bubble to the surface, reuniting with Sandy. Back aboard the Texas Rose, Fenn and Grogan are pinned down by the cabin boy’s revolver, and Sandy reveals Daniels’s betrayal: it was he who shot the Professor to keep a profit-driven plan alive. Daniels tries to seize control, but the mutineers lock him and his captive allies away with the Professor. Just as the truth comes to light, the Sentinel swallows the ship in a final, devastating assault, crushing Daniels beneath a statue while the rest launch into the lifeboat, leaving Atlantis’s island world behind and the mystery of their uncharted voyage unresolved.