Rowenna Michaels and Julie Sands, two archaeologists in the Kilgai Gorge, stumble upon a modern human skull buried in strata older than the first known homo sapiens. When they return to investigate, however, they find that UNIT has placed the gorge off limits. Rowenna finds the corporal in charge, Jacob Hynes, very off-putting in a dangerous way, and decides to call her old friend Jo Grant for help. But as Julie is making the call she and Rowenna are attacked and kidnapped by Hynes -- and the horse-like alien he’s working for. Jo hears the interrupted call on her answering machine, and sets off to investigate, leaving her son Matthew with her former husband Cliff. Her old friend Sergeant Benton admits that Hynes has called for backup to deal with an unspecified threat of some sort but is reluctant to let Jo involve herself. Eventually he agrees to let her go to Kilgai Gorge as an observer, but after she’s gone he double-checks Hynes’ credentials -- and finds that although he has a full service record in the computer, it isn’t backed up in microfiche...
The Doctor and Sam set course for London in the year 2109, still seeking back issues of the Strand to complete the Doctor’s collection, but they instead arrive in the middle of a swamp. Two horse-like aliens, Tractites named Kitig and Narunil, come to their rescue and invite them to shelter in the local city Afranis while their “re-entry vehicle” is repaired. The Doctor and Sam soon realize that they’re in an alternate Universe where the human race never existed -- and for reasons the Doctor doesn’t fully understand yet, this timeline is unstable and will soon collapse in upon itself, destroying the entire fabric of reality. Although “Paratractis” is much more peaceful and benevolent than any human civilisation, he has no choice but to find the point of historical divergence and correct it, thus preventing Paratractis from ever having existed.
Jo arrives in Kilgai Gorge, only to be held at gunpoint by Hynes and taken to the nearby caves. There, Rowenna and Julie are being held captive by a Tractite, Gavril, who has infected them with a disease which will wipe out all of humanity. Hynes believes that it is his destiny to destroy the human race, but as he rants insanely Jo is able to release Rowenna and Julie from their bonds. As they flee, Hynes and Gavril try to stop them, and in the confusion they stumble into the “time tree” which Gavril and Hynes were using. Jo, Jacob, Rowenna and Julie are all transported two and a half million years back through Time.
The Doctor finds Tractite books telling of the near-destruction of their race by a mythical species called “humans” -- and of a being called the Uncreator who will destroy all of Tractite civilisation. Kitig is in fact the Keeper assigned to watch for the Uncreator and destroy him, but he’s also a kind family man who feels it’s his duty to watch wisely and prevent unnecessary deaths. Despite the mounting evidence he refuses to kill the Doctor, who seems a kind and gentle man, until his guilt is made clear. The Doctor, recognising the danger he faces, fakes a seizure in order to get back to the TARDIS, where he finds that the Universe has already begun to collapse. Before he can stop her, Sam calls Kitig into the TARDIS to safety despite the Doctor’s warning that Kitig will never have a Universe to return to. The only safe places now in all time and space are the TARDIS and the focal point from which the divergence occurred.
The Doctor takes the TARDIS back through Time, and Sam disobeys him and follows him out -- and Kitig follows as well, having decided that he must complete his duty and kill the Uncreator in order to return home. The Doctor finds the time tree; Jo has gone to fetch water, and Rowenna and Julie are waiting for her to return. The Doctor takes a blood sample from Julie in order to analyse it and find a cure for the virus, but Jacob, who has been hiding nearby, attacks him, steals the hypo and sets off to find a homo habilis settlement and spread the infection. The Doctor pursues him but loses him when Kitig attacks and tries to kill him; but before Kitig can do so they hear the women screaming in the distance. Kitig and the Doctor rush to their aid but are too late to prevent them from being torn apart by a pack of wild dogs. When Kitig sees the Doctor’s grief over their deaths he realizes that the Doctor is a good man who has been telling the truth all along.
Jo returns too late to help her friends, but the Doctor gives her a new mission; find Sam and stop Jacob. He must go further back in time, as there is another possible focal point from which history will diverge; the disease Hynes plans to release is capable of destroying all mammalian life, and since there were mammalian species existing on Paratractis, that means its history must have diverged at an earlier point. The Doctor and Kitig return to the TARDIS and locate another stable focus a million years further back in Time. There, they find a Tractite settlement established by the ruthless Mauvril, survivor of the Earth Empire’s invasion and purge of Tractis following a failed rebellion. Mauvril became a resistance fighter and killed many humans before discovering the time tree, which enabled her and her people to travel back in Time. Gavril was lost along the way and apparently tried to complete his mission with the help of the mad Jacob and a seedling from the time tree. The others, meanwhile, came back to the dawn of human history to establish a colony and prevent the human race which destroyed their world from ever having existed.
The Doctor tries to warn Mauvril that her plan is doomed, since the time tree is organic; it draws its energy from the Universe, and thus cannot create a new one -- it can only force an unstable divergence which has already begun to collapse. Only the Doctor and the TARDIS are keeping this timeline stable. But Mauvril, certain that the Doctor is an Imperial agent, places him under arrest and drops the TARDIS into a volcano. She can’t bring herself to harm the innocent Kitig and allows him free run of the settlement. He tries to forget about the Doctor at first, but then he stumbles across the remains of a human village which was wiped out by the Tractites when they travelled back through Time. Kitig realizes that Paratractis was founded by killers who are already covering up this part of their history, and upon confronting Mauvril, learns that she’s locked the Doctor up for days without food or water. Disgusted, he takes his leave of the other Tractites and goes out into the wilderness to carve a message from the Doctor into the rocks of the mountain.
Sam meets Jacob, who claims to be working on behalf of UNIT to cure the nearby habiline settlement of a deadly disease. Thanks to the TARDIS, Sam is able to communicate with the habilines, and she tries to convince them that she and Jacob are here to help. When Jacob tries to inject the habiline “Axeman” with the hypo Axeman resists, and Sam helps to inject him -- but then Jacob flees, laughing, leaving Axeman to kill Sam. Jo arrives just in time to save her, and Sam learns too late that she’s just infected the habilines with a disease which will destroy the entire human race. Sam and Jo shelter in the wilderness for days, waiting for the Doctor to return and help, while Jacob prowls the savannah, growing ever more feral. Eventually he attacks Sam and Jo, but Axeman finds and kills him and begs for the women’s help. Sam herself is starting to succumb to the disease, but she and Jo find the fossilised remains of Kitig’s million-year-old message. They follow the message to the TARDIS, which is buried within the fossilised volcanic basalt; but the interior of the TARDIS is shrunken and dead...
Mauvril keeps the Doctor alive to tell her story to him, trying to justify her actions. But he manages to escape, and, sensing the TARDIS calling to him, sends it a mental command which brings it to life a million years in the future. Sam and Jo are thus able to enter the ship, find curative tablets for Sam and return to him. In the fraught confrontation which follows, Mauvril shoots and kills Axeman, and Sam panics and shoots a Tractite which was running towards her, gun in hand. As Jo and Sam shelter behind a Tractite laser cannon, the Doctor tries to convince Mauvril to let him use the TARDIS to take her people to a new world where they can really make a fresh start. But just as it appears he’s convinced her, somebody shoots at Jo and Sam -- and Jo opens fire with the laser cannon, killing the Tractites and destroying the entire Paratractite settlement. The Doctor is horrified, and neither he nor Sam knows whether Jo panicked or deliberately killed the Tractites so she could return home.
Kitig returns too late to help, but accepts that there was nothing he could have done to change things. Instead, he agrees to remain on prehistoric Earth to finish carving the messages for Sam and Jo. The Doctor takes Jo home, provides a vaccine for the habiline settlement, and then takes Sam into the future to deal with the Empire and restore Tractis’ independence. Kitig spends the rest of his life carving messages for Sam and Jo until he’s too old to carve any more, and then takes the time tree back to the creation of the solar system, ensuring its destruction.