The TARDIS lands on a seemingly deserted volcanic island. The 2nd Doctor, Ben ,Polly and new recruit Jamie are captured and taken in a lift down a very deep shaft that leads well below the seabed.
They are prisoners of the survivors of Atlantis. Their High Priest, Lolem, declares they are to be sacrificed to the great god Amdo, as they are about to be fed to a pool of sharks Professor Zaroff arrives. He is a renegade scientist who devised the technology from which the plankton food the Atlantians live on has been refined. The Doctor succeeds in persuading the Professor to hire him for his scientific staff. They are all in the lost city of Atlantis - but Zaroff has a plan to raise it from the sea.
Jamie and Ben are sent to work in a mine, while Polly is marked out by scientist Damon for conversion through surgery into a Fish Person, one of a band of genetically and surgically altered amphibians that farm the plankton for the city.
The Doctor interrupts the electricity supply, thereby postponing the conversion operation. Damon blames Zaroff. Zaroff is obsessed with raising Atlantis from the sea, planning to drain the sea away into the Earth’s core as a means to restore the land mass to the surface. This will generate vast amounts of steam which will crack the Earth’s core and destroy the planet. Zaroff tells the Doctor that this is his ultimate aim! Polly is freed by a servant girl named Ara, and the Doctor escapes from the laboratory.
Ben and Jamie have been placed to work in a mine where they meet two ship wrecked sailors similarly confined, Sean and Jacko. All four escape using a secret mine shaft which emerges in the temple of Amdo – where Polly is hiding. Ara protects them, providing food and hiding them from the guards.
The Doctor meets a priest named Ramo who is resistant to the influence of Zaroff on the Atlantean court, he warns him that Zaroff really means to destroy Atlantis. Ramo smuggles the Doctor before Thous, King of Atlantis, so that he can voice his warning. The King believes in Zaroff and hands the Doctor and Ramo over to him as prisoners.
The Doctor and Ramo are taken for execution at the Temple of Amdo where Lolem is given the opportunity to make another sacrifice. However, a ruse by Polly and the others convinces the priests that a statue of Amdo has found voice. The Doctor and Ramo are spirited away into a secret room behind the statue while Lolem believes his god has swallowed the offering. When Lolem reports this miracle at court Zaroff denounces it, insulting Amdo and sowing seeds of doubt in the mind of King Thous.
The Doctor decides to cause a revolution by creating a food shortage. He realises the plankton-based food will not last long before perishing, so decides to cause its farmers to stop supply. Sean and Jacko are sent to persuade the Fish People to revolt. They succeed in causing a production strike relatively easily.
The Doctor and his friends head off to tackle Zaroff himself. The Doctor disguises himself as a gypsy soothsayer at the Atlantean market and helps trigger a ruse to separate Zaroff from his guards. Zaroff is captured by the Doctor’s party and taken to the secret room behind the statue, where the crazed man boasts his plan is unstoppable. Having faked a seizure, Zaroff manages to get hold of a trident and stabs Ramo, who has been left to guard him. Ramo survives, but is badly wounded, while Zaroff escapes. The megalomaniac has found his loyal guards and returns to the royal court mob handed, where he confronts Thous. The King is aggrieved by the strike among the Fish People and has lost his faith in Zaroff to raise Atlantis from the sea. Zaroff responds by shooting Thous, while his guards take on the royal protectors in pitched combat. In Zaroff’s own words, “Nothing in the world can stop me now.”
With Zaroff gone, the Doctor finds Thouss bleeding but alive in the throne room and has him taken to the secret chamber for safety. He then determines to flood the lower portion of Atlantis so that the reactor and Zaroff’s laboratory are destroyed. Sean and Jacko are told to alert the Atlantean populace to flee to the higher levels, while the Doctor and Ben head to the generator station to put the plan in motion. Once there they cut through cables to render the reactor unstable. All over the lower portions of Atlantis the sea walls start to perish. Jamie and Polly are caught in the flow but succeed in swimming to safety. Sean, Jacko, Thous and a pentinent Damon are also fleeing the lower reaches of the city, though Lolem is missing, presumed dead.
Zaroff has now become totally mad, obsessed with his scheme to destroy the Earth. Ben and the Doctor confront him and, with the city in ruins, his guards and technicians all flee. With the water level in Zaroff’s lab rising, Ben succeeds in trapping the madman behind a grille to prevent him reaching the detonation controls. Zaroff drowns while the Doctor and Ben flee, unable to help him.
After a long slog they make it to the surface and are there reunited with Jamie and Polly. Knowing that some of the Atlanteans, including Thous, Sean and Jacko, will have survived, the quartet return to the TARDIS and the Doctor operates the controls. They are only just taking off, however, when an external force seizes the craft hurls them uncontrollably around the console room.