The TARDIS begins to disintegrate in mid-flight, responding to the Doctor’s sudden, inexplicable conviction that he is dead. Benny falls through the cracks in the ship and is expelled into the Vortex, while the Doctor and Ace retreat to the secondary control room. They are nearly crushed when the TARDIS closes in around them, but it rights itself at the last moment and materialises. The Doctor recovers, and he and Ace emerge to find themselves in what appears to be a Jurassic jungle. As they explore further, however, they find plants from different, widely scattered time zones, and the TARDIS is attacked by an irritated edmontonia and pushed into a tar pit. Assuring the worried Ace that the TARDIS can take care of itself, the Doctor takes her to a nearby outcropping to avoid a herd of migrating seismosaurs, but as they watch, a feral human woman bursts out of the undergrowth -- and the Doctor recognises her as his former companion Jo Grant. Ace notices hunters in the distance, riding dinosaurs in pursuit of Jo, and as they draw nearer the Doctor realises that the hunters are Silurians…

As the Doctor helps the feral Jo to escape, Ace succumbs to race-memory malaise and flees in panic. The Doctor and Jo are rescued and taken to Cheddar Gorge, where a hidden community of humans struggles to survive and protect themselves under the leadership of a bitter Brigadier Lethbridge-Stewart. The Brigadier isn’t terribly surprised to find that the Doctor has returned from the dead, but he doesn’t know whether he can trust this new, ambiguously motivated incarnation of his old friend. Jo falls into a coma, and Dr Sam Meredith finds that she was pregnant and suffered a miscarriage in her flight from the hunters -- but despite her grievous internal injuries, she still completed her journey to Cheddar Gorge, clutching a half-pamphlet which the Brigadier now refuses to let out of his sight.

The Silurian hunters are still on Jo’s trail, for Imorkal, the hot-headed young son of the Silurian leader Morka, refuses to abandon the hunt without a trophy. Despite the advice of his bodyguard Vronim and mentor Chtorba, he presses on and discovers evidence of the human base at Cheddar Gorge. The humans attack the Silurians to prevent them from taking news of their discovery back to their own people, and Vronim is killed in the fighting. The wounded Imorkal hides himself in the dead body of the dilophosaurus he had been using as a mount, and when the humans give up the search and retreat, he sets off for the old bunker on Wenley Moor, intending to call for help. Meanwhile, the Doctor stops the Brigadier from cold-bloodedly shooting the injured Chtorba, and tries to convince him to take this opportunity to make peace. But twenty years of struggling to survive in the Silurians’ world has hardened the Brigadier, who is now convinced that the only way to make the world safe is to destroy the Silurians.

Ace finds her way to the ruins of Bristol, where she nearly falls form the decaying suspension bridge when the rusting support struts snap in her grip. A search party finds her and takes her back to Cheddar Gorge, where the Brigadier has decided to send Dr Jan Martin and Sergeant Benton to London to find medical supplies for Jo. The Doctor tells Ace to join them; there’s something he wants in London, but he must remain in Cheddar Gorge to help Liz Shaw build a telepathic dampener which will counter the effect of the race-memory malaise… and to keep an eye on the Brigadier. As the Doctor and Liz work, she tells him that his former self disappeared from Wenley Moor after the Silurians released the plague upon Earth and destroyed most of its human population. The Doctor begins to wonder whether he unknowingly used his powers as a Time Lord to change history; was he meant to die, and did he arrogantly create a whole new timeline just to ensure his own survival? He concludes that this is not possible, as he’d already seen the future of Earth in his personal past; it must be this Universe which is false, and somehow, someone has brought it into existence. But this is a problem for another time; here and now he must deal with the immediate situation. Thus, he attempts to steal the Brigadier’s pamphlet, and when he fails he flees from the base -- taking Chtorba with him. He hopes to convince Chtorba to negotiate a lasting peace, but instead, Chtorba takes him to the Silurian city which was once Glasgow, and alerts his people -- who prepare to attack Cheddar Gorge.

The Brigadier, desperate to find the rest of the pamphlet, deliberately administers a drug overdose to Jo, hoping to wake her and find out where she has been. Instead, she dies. However, he finds the answers he seeks in the rubbish bins where Jo’s clothing was thrown when she was first brought to the base. Meanwhile, the expedition to London arrives in a city overgrown with primeval vegetation, and roamed by packs of feral dogs and humans suffering from race-memory malaise. The Silurians are remaking the world in their own image, using genetic engineering and atmospheric control, and soon there will be nothing left of the human race at all. Julia is bitten by a wild dog and infected with mutated rabies, for which there is no cure; nevertheless, she continues on with the expedition to an abandoned hospital, where they scavenge as many medical supplies as they can. Bored, Ace tries to restart one of the cars in the parking lot -- but the noise brings every Silurian in the area on the run. In the battle which follows, Ace and Alan are separated from the others, and Ace dumps two Silurian bodies into the hospital furnace to prevent the other Silurians from finding them, only to realise too late that one was still alive. Julia gives her life to hold off the Silurians while the others escape, but the Brigadier then calls Benton with new instructions. Benton refuses to return to Cheddar Gorge with the medical supplies until his new mission is complete, and Jan and Rod set off by themselves, leaving Benton to carry out his new orders alone.

Chtorba accompanies the Silurian attack force to Cheddar Gorge, and although the Doctor still tries to negotiate peace, the force’s leader Chtaachtl refuses to listen to him, a mere mammal. The Doctor is thus forced to watch helplessly as humans and Silurians begin to slaughter each other once again. Chtaachtl has the Doctor locked up as the attack continues, but Benny unexpectedly surfaces and rescues him. Before she can explain how she came to be on the airship, the humans attack and capture it, and in the confusion she and the Doctor are separated once again. Benny escapes from the ship on a tame pterodactyl, but collides with a microlight glider flown by a human soldier, and crashes to the ground. The Silurians, unprepared for the ferocity of the humans’ attack, are forced to retreat, and the Brigadier triumphantly proclaims victory -- until he sees Liz sobbing over the body of a young child who was killed in the fighting.

Ace and Alan escape from the hospital, but before Ace sets off on her own mission for the Doctor she stops off at an old friend’s house -- and discovers that in this reality, Manisha is still alive, at a city farm where humans eke out a living hidden from the hunting Silurians. Manisha helps Ace and Alan to fetch the TARDIS from what used to be UNIT HQ, and the founders of the city farm loan Ace their one remaining Jeep so she can take it to Wenley Moor. On their way, however, they encounter Imorkal, who uses his third eye to attack Alan, causing the Jeep to crash. Ace and Manisha manage to knock Imorkal out, but Alan is suffering mortal internal injuries and he begs Ace to shoot him. She does so, and the appalled Manisha must then stop her from killing Imorkal in cold blood. They manacle Imorkal to the Jeep and continue on foot, but Imorkal recovers and uses his third eye to snap the lock of the manacles. Unaware that they are being pursued, they make their way to Wenley Moor, the cyclotron, and the remains of the old Silurian hibernation chamber -- where the body of the Third Doctor remains in his cell, clutching the TARDIS key in his skeletal hand.

Chtorba and the Doctor survive the attack on Cheddar Gorge and travel to the new capital city of Earth -- Ophidian, in Africa. There, the Doctor is reunited with Morka, the leader of the Silurians, who has mellowed with age and now understands the horror of the crimes he committed in his youth. He reveals that when Benny fell into the Time Vortex she emerged in Ophidian, where she was captured and experimented upon -- and that through her, Morka and his scientists finally found a viral cure for the race-memory malaise. Benny was smuggled aboard the airship and sent to Cheddar Gorge to release the cure back amongst the human population, so that humans and Silurians would finally be able to co-exist in peace. But when Chtaachtl, Morka’s mate, learns that he has done, she is furious; the humans captured an airship during the attack, and once free of the race-memory malaise, they will be able to study the Silurians’ technology and turn it against them.

The Brigadier apparently intends to used the captured airship to stampede dinosaur herds across Ophidian, but when Jan arrives with the medical supplies and learns what has happened to Jo, she accuses the Brigadier of clinical megalomania and tries to use her authority as medical officer to remove him from power. Before she can do so, however, Benton returns with the other half of the Brigadier’s pamphlet, restoring the Brigadier’s confidence; with this booklet, the war will soon be over. He sends a coded message to the waiting General Hobson, arranging a private meeting, and the suspicious Benny follows him to Avonmouth, where she sees a submarine rise from the sea. This is the last surviving British nuclear submarine, the HMS Revenge, and the Brigadier now possesses the firing codes for the sub’s missiles. He gives the booklet to Hobson and prepares to return to Cheddar Gorge to lead the decoy attack on Ophidian, but on the way he sees another horse tied up nearby, and realises that he was followed. He thus contacts Hobson one last time, and Benny is found and arrested. She escapes, takes a rating hostage and forces him to lead her to one of the missiles, which she threatens to detonate inside the sub unless Hobson returns to land and defuses the remaining missiles. Her hostage, however, has deliberately led her to the one dud missile, and more ratings storm in and shoot her in the chest as she presses the useless detonation button.

Morka uses a telepathic link to show the Doctor his memory of the Third Doctor’s murder, and to apologise for his past actions -- but then goes into convulsions, sensing the distant death of his son. Imorkal has caught up with Ace and Manisha in the ruins of the Silurian base, where Ace uses the Third Doctor’s sonic screwdriver to defend herself -- but suffering from race-memory malaise and unsure how to operate it, she accidentally pulverises Imorkal’s brain with the sonic pulses. Chtaachtl, blaming Morka for the death of their son, locks up the Doctor until the scientist Ichtar can get around to dissecting him, and orders that Wenley Moor be destroyed in retaliation. Ace and Manisha rush back to the Third Doctor’s TARDIS as the Silurians use their atmospheric control to focus a blast of sunlight onto the moor. The TARDIS collapsed in upon itself when the Doctor died, but Ace -- who is telepathically keyed to the TARDIS due to her travels with the Seventh Doctor -- uses the Third Doctor’s key to restore its interior based upon her memories of the other one. Before she can do anything with it, however, she and Manisha collapse from heat exhaustion.

The Revenge is attacked by Sea-Devils, who send a warning to Ophidian; but as Chtaachtl and Morka prepare their response, the Brigadier and his men begin their attack and dinosaur herds stampede across the city, causing chaos. The Doctor manages to escape and tries to return to the palace, but on the way he sees a Silurian child crushed to death in the stampede. Benton is killed in the fighting, and the Brigadier and Liz are captured and brought before Morka. As the two enemies confront each other, the Doctor arrives, carrying the dead child’s body in the hope of making them see sense; but the Brigadier announces that this attack was only a diversion, and before the Silurians can destroy the Revenge it launches its missiles at Ophidian. Benny is amongst those who evacuate before the sub is destroyed, leaving her surrounded by Sea-Devils, stranded with a punctured lung on a life raft in the middle of the ocean.

Ace recovers just in time, and following the Doctor’s earlier instructions she programmes the TARDIS to materialise around the entire Earth. It does so just as the missiles reach Ophidian -- and since the TARDIS is in a state of temporal grace the missiles fail to explode. A door to the console room opens in Morka’s palace, and the Doctor enters and reprogrammes the architectural configuration, moving the wounded Benny to Ophidian and deleting those parts of the city which contain the nuclear missiles. The TARDIS is breaking up under the strain, and in the chaos Ace realises that the Doctor has nearly programmed the TARDIS to delete everything but the warheads. He corrects this, completes his work, and rematerialises back in the palace, where the tremors caused by the strain to the TARDIS have nearly toppled the egg of Morka’s next child from its pedestal in the throne room. The Brigadier has caught it and is threatening to destroy it -- but, faced with the body of the dead Silurian child, he realises that he is holding another child in his hands and finally realises what he has become. He agrees to discuss peace with Morka, at long last.

The Doctor and his companions depart in the alternate TARDIS, leaving this parallel Earth to a brighter future… or so Ace and Benny think until the Doctor informs them that it will have to go. Someone tampered with history to make this world, somehow preventing the Third Doctor from regenerating when Morka killed him. This timeline is an artificial creation, and as there is only a limited amount of energy available to the real Universe, its existence means that the real timeline will now end billions of years prematurely. In order to restore the balance, the Doctor must use this TARDIS to Time Ram the one in the tar pit, and redirect the energy release to destroy this Universe. Ace storms off to her room in disgust, while Benny, although upset, nevertheless accepts the Doctor’s argument that this must be done. The Doctor prepares to Time Ram his old ship, vowing to track down his new enemy and bring him to book for his crimes -- whoever, or whatever, that enemy may be.