The year is 1934. According to legend, the Polynesian island of Salutua disappeared after a fire god rose up from the volcano and drove away the natives. However, the eccentric Professor Sternberg believes that he’s located the legendary island, after tending to a man found floating in the Pacific Ocean with giant animal bites on his body. An American millionaire, film producer Marshal Grover, funds an expedition to Salutua based on Sternberg’s findings, apparently intending to use the island as a backdrop for a realistic monster movie. The expedition’s ship, the Constitution, passes through what appears to be a freak atmospheric distortion which shrouds Salutua from the outside world, but is disabled by an underwater explosion as it enters the lagoon. The crew successfully beach the ship, and as they begin to conduct repairs, Grover’s team sets off to explore the jungle. The flora and fauna on the island prove to be impossibly gigantic, but Grover’s spoiled second wife, former starlet Nancy Norton, is terrified by the unnatural growth, and when she’s attacked by a giant snake she flatly refuses to film anything on the island. Grover, however, refuses to take her away just yet. He has another reason for coming to Salutua -- a motive connected to his beloved daughter Amelia, who lost an arm in the car crash which killed Grover’s first wife.

In present-day London, the Doctor and Liz are working on the TARDIS console when Sergeant Mike Yates arrives in the laboratowy with a package from UNIT’s Australian bureau, a fragment of an alien spaceship found in the belly of a shark. The Doctor tunes the TARDIS’ Space-Time Visualiser to the frequency of the omicron radiation trace on the fragment, and creates what appears to be a holographic image of the fragment’s path through history, terminating at the moment of its creation. As Yates leaves to report to the Brigadier, however, Liz realises that the “image” is in fact a time bridge, through which solid material can pass; the Doctor is in fact making another attempt to escape from his exile. The Doctor passes through the bridge to explore the island on the other side, but the Visualiser’s power accumulators begin to overload. While trying to warn him, Liz accidentally falls through the time bridge and is stranded on the other side with him when the accumulators short out.

Grover’s cameraman de Veer, trying to get one up on the selfish Nancy, suggests using Amelia as a stand-in for long-shot location footage. Nancy, who fought her way to stardom from the slums, has become paranoid about any perceived threat to her livelihood, and that night she confronts Amelia privately on the ship’s deck, convinced that Amelia is trying to steal the picture from her. As Amelia tries to explain that this is not the case, the ship is attacked by giant crabs, and when Nancy tries to escape she accidentally knocks Amelia overboard. Surrounded by the crabs, Amelia is forced to retreat into the woods, and Grover and a team of sailors set off to rescue her, while Nancy remains on the boat, paralysed by guilt and self-reproach. In the forest, Amelia manages to escape from the pursuing crabs, but then falls into a giant pit masked by vegetation, and is unable to climb out.

The Doctor and Liz explore their surroundings, and discover that they’re in the caldera of a dormant volcano. An alien spaceship is embedded in the ground, and a device powered by geothermal energy from the volcano is generating a force field that renders the island invisible to the outside world. The Doctor theorises that the device has caused the volcano to cool down and lapse into dormancy, which means that the ship must have been here for quite some time. He and Liz then hear gunfire and screaming from the jungle, and investigate to find that the rescue team from the Constitution has been caught in the middle of a battle between giant crabs and giant bats. The crewmen are being slaughtered until the Doctor arrives with his sonic screwdriver, which drives off both the bats and the crabs. The Doctor claims to be from a British expedition, and although wary of rivals, Grover is grateful for the Doctor’s help. It is now obvious that the search for Amelia will have to wait until morning, and the Doctor and Liz accompany the team back to the Constitution. On the way back, they spot strange marks in the jungle earth, which appear to be the tracks of a miniature tank.

Back at UNIT HQ, Sergeant Osgood manages to repair the time bridge, although it must be run at a reduced rate of power in order to prevent the accumulators from burning out again. Yates volunteers to go through the bridge and search for the Doctor and Liz, and while searching the island, he finds Amelia and rescues her from a giant spider. Since Amelia is unable to climb out of the pit, she and Mike must search for another way out, and while doing so they stumble across a giant statue, presumably the islanders’ deity -- a giant humanoid carved from remarkably pliant stone, with a single ruby-red eye. The pit turns out to be an extinct lava tube, which comes to the surface elsewhere in the jungle. While returning to the Constitution, however, Mike and Amelia are attacked by a miniature tank which has been taking samples of the flora and fauna from the island. Trying to fight it off, Mike accidentally destroys it when his grenade ruptures what proves to be a high-pressure water tank. He and Amelia are then reunited with the expedition members and with the Doctor and Liz, but as they share stories, a shower of paper leaflets floats across the island, having been flung through the time bridge by a desperate Lethbridge-Stewart. UNIT’s research team has just learned that Salutua will be completely destroyed by a volcanic eruption this very night.

The Doctor is forced to admit the truth, but Grover refuses to abandon his expedition on the word of people who claim to have travelled through Time. In order to prove his story, the Doctor suggests that Mike show Grover the “statue” in the pit, which the Doctor believes is in fact a dead alien in a life support suit. Upon arriving at the pit, the Doctor studies the statue for himself and finds a storage unit containing two Semquess drug vials and one empty space; he concludes that the third vial must have broken open in the past, releasing chemicals which resulted in the gigantism on the island. He intends to dispose of the other two, but before he can do so, Grover has his men hold the Doctor, Liz and Mike at gunpoint and seizes the vials, revealing that he came to the island in the hope that the cause of the unnatural growth could be tamed to grow back Amelia’s missing arm. Nancy, who has been suffering from guilt ever since Amelia fell into the water, realises that this entire expedition was for Amelia’s benefit and not her own, and in a fit of rage she lashes out at Amelia’s self-righteousness -- infuriating Grover and destroying herself in his eyes before she realises what she’s done.

The Brigadier finds that he is unable to pilot the time bridge beyond the caldera, since it is tuned into the omicron radiation signature from the spacecraft. Benton thus prepares to lead a team through the bridge to find and rescue the Doctor, Liz and Yates. As the team prepares to set off, reports start to come in from UNIT’s American offices of strange, spectral UFO sightings on the American west coast. Sightings are also reported of ghosts and of spectral buildings which have not existed for years. Soon reports are coming in from all over the American continent, and then from Hong Kong and Japan. As Benton and his team pass through the time bridge, a commercial jet crashes in Munich after the pilot reports that the runway has changed position. Soon the sightings reach England as well; ghostlike squadrons of marching figures, dead people and condemned buildings are spotted. The opposite occurs as well -- people who still exist become harder to perceive...

Grover has the Doctor, Liz and Mike locked up on the Constitution, promising to release them before the volcano erupts so they can return to their own time. The Doctor, however, refuses to help Sternberg open the vials, claiming that the human race is not prepared to handle the alien technology within. Amelia, who believes that the loss of her arm is a test from God, accepts the Doctor’s argument and refuses to take any of the drugs even if Sternberg somehow manages to open the vials. Meanwhile, Nancy, knowing that her marriage to Grover is effectively over, seduces crewman David Ferraro and convinces him to steal the giant’s ruby eye from the pit. When he fails to return, she goes looking for him -- to find that he has been hypnotised by the ruby eye and is building a fire in the pit. Before Nancy can respond, the heat restores the giant to life, and it hypnotises her as well. The smoke from the fire attracts the attention of Grover’s men and of Benton’s search party, but when they arrive, the giant, Brokk, holds Nancy hostage and uses her as its telepathic go-between to demand the return of the ampoules. He had stolen the vials from the Semquess, but they shot down his ship and he crashed on this relatively cold planet, losing one of the ampoules in the process. He drove away the natives of the island and installed the force field to prevent the Semquess from finding him while he repaired his ship, but first he went searching for the missing ampoule and fell into this pit, damaging the heat exchanger of his survival suit. He has been trapped, dormant, for fifty years, and in the intervening time the Semquess have tracked him down. The miniature tanks are the Semquess’ life support units, they have been taking samples from the island to determine whether their drugs are responsible for the growth here, and it was presumably a Semquess tank which struck the Constitution in the lagoon, damaging the ship.

Realising that the Doctor was right all along, Grover orders the reluctant Sternberg to surrender the vials, but just as they are handed over the Semquess tanks arrive. As Brokk still holds Nancy hostage, the UNIT troops are forced to fight off the Semquess while Brokk escapes, but the Semquess mothership then emerges from the lagoon, and Brokk realises that he will never escape them. Following him at a distance, the others see him place Nancy down and continue on to the ship alone. Realising what is about to happen, the Doctor sends Grover’s group back to their ship and tells the UNIT team to assemble on the beach. Benton has left one man standing by the time bridge, and the Doctor has Yates radio instructions to him to pass on to the Brigadier. Brokk’s ship takes off, but the Semquess shoot it down, and its fragments are scattered across the island -- thus covering the island in omicron radiation and enabling the Brigadier to pilot the time bridge to the beach. As the UNIT team escape and the repaired Constitution heads back out to sea, the nuclear core of Brokk’s ship plunes into the heart of the volcano, triggering an eruption which destroys Salutua and scatters the fragments of Brokk’s ship throughout the surrounding area. One day, one of these fragments will be found and eaten by a shark.

Back in present-day England at last, the Doctor begins to power down the time bridge -- but suddenly the power in UNIT HQ goes out, and Yates sees that the lights of London have changed outside the window. Realising what has happened, the Doctor stops before shutting down the time bridge completely. Salutua must have existed on a nexus point in time and space, and by passing through the bridge and interfering in the past the Doctor and his friends have changed history. While the time bridge was operating at full capacity the two timelines co-existed side by side, causing the spectral sightings which began on the opposite side of the world and have slowly been approaching the terminus of the time bridge. Since UNIT HQ’s electrical generators no longer exist, the time bridge only has a limited amount of power, and when that runs out the time bubble preserving this corner of UNIT HQ will be wiped out of existence. The Doctor and his companions must find out how history has changed, return to the Constitution, and fix things before their timeline ceases to be.

UNIT HQ is attacked by soldiers in unfamiliar uniforms, who capture Liz and take her through the interface into the other timeline. The Doctor knows that she will only survive for a short time on the other side; she is currently imbued with artron energy due to her trip through the time bridge, but as that decays she will slowly cease to exist. The Doctor, the Brigadier and Benton set off after her, using the fragment of Brokk’s ship from the time bridge as a portable artron energy reserve. Yates and Osgood remain on guard as the soldiers outside begin to bomb UNIT HQ; their bombs fade away on UNIT’s side of the interface, but are slowly becoming more real -- and more dangerous.

Liz is taken through a version of London which resembles the futuristic visions of old silent films. In what used to be St Paul’s Cathedral, she is questioned by nuns dressed in scarlet, who open a satellite to this world’s Goddess -- Nancy Grover. Nancy reveals that Brokk, knowing he could not escape the Semquess, struck a deal with her and gave her the Semquess vials and fragments of his brain-eye. The figure that boarded the ship and took off was just the husk of his body, acting autonomously. Since Nancy was unable to hide the ampoules in her pocketless dress, she had Sternberg smuggle them aboard the ship; unwilling to leave Salutua without some proof of his discoveries, he was happy to do so. Once aboard the ship, however, Nancy murdered him and used the contents of one ampoule to merge herself with a fragment of Brokk’s brain-eye. Using the powers granted to her by the ruby fragment, she took over the minds of her maid Tilly and the disgraced David Ferraro, planted ruby fragments in their foreheads as well, and proceeded from that point; once Grover’s films made her a star, she was able to spread her mesmeric influence over the world and reshape it in her image. Now she is the star she’s always wanted to be, and the Goddess of a world; the people of her Earth have already fought off the Semquess, and soon they will have constructed a new body for Brokk. However, Liz realises that while this world is united rather than divided, it is ruled by fear, and when Nancy loses the powers granted to her by her union with Brokk, her utopia will fall.

Infuriated by Liz’s rejection, Nancy attempts to bring her under mental control, but fails when Liz begins to fade from existence. Fortunately, the Doctor arrives just in time, and once back in the time bubble surrounding Bessie, Liz returns to normal. The Doctor drives back to UNIT HQ, and as Nancy’s soldiers redouble their efforts to destroy the time bridge, he leads the Brigadier, Benton and Yates through the time bridge to the Constitution to face Nancy in the past. Nancy and her slaves are in the process of taking over the ship, and when they attempt to kill the intruders, the Doctor -- realising that Nancy is beyond reason -- uses his sonic screwdriver to find the resonance point of the ruby crystals. The crystals shatter, killing Tilly and Ferraro, but as Nancy dies she falls atop the ampoule -- and the contents spill over her body, the remaining ruby fragments, and the structure of the Constitution itself. Back at UNIT HQ, Liz and Osgood find themselves looking out over a devastated wasteland as the Constitution begins to warp into a monstrous living being. The contents of the ampoule have merged Nancy, Brokk’s eye, and the organic components of the ship itself into a voracious living entity, part animal, part vegetable, and part mineral; the transition has driven the new entity insane, and it will consume all life on Earth.

The Doctor is unable to fight this new life form, and when Liz and Osgood try to cut it to pieces using the time bridge, the pieces reconstitute on the other side and attack them. They are forced to flee beyond the interface, but begin to fade away once outside the time bubble. As the Constitution prepares to devour its passengers, the Doctor realises that his only remaining weapon is the third ampoule -- the most dangerous and valuable of all, which releases the full potential of any life form which consumes it. He is unwilling to risk the consequences of his drinking it, fearing what he might become -- and before anybody can stop her, Amelia grabs it from him and drinks it herself. The shock of the chemical transformation kills her, but her faith and the powers of the transformation enable her to survive beyond death, turning her into an angelic being with all of the powers that implies. The new Amelia subdues the hybrid life form, and promises to care for it until she can find a way to separate Nancy and Brokk once again. Realising that she no longer belongs on Earth, Nancy bids farewell to her tearful father and sets off to explore the Universe and try to understand her new purpose in it. The Doctor and the UNIT team return to London to find that, apart from a few newspaper headlines regarding the fate of Grover’s expedition, history has returned to normal.