The Doctor’s plans to visit the planet Kegron Pluva are postponed when the TARDIS detects temporal distortion; somebody has travelled to early 21st-century Bromley using a dirty rip engine, a dangerously primitive form of time travel that is usually outlawed by whichever civilisations have survived discovering it. The TARDIS materialises in a park, and while the Doctor and Jack scan the city for the source of the time distortion, Rose visits the local nail salon, chats with the manicurist, and learns that a man dressed as a caveman was recently taken to Southam Hospital after getting involved in a bar brawl. The Doctor takes the TARDIS to the hospital, but finds that the army has moved in and are evacuating the staff and patients. While Jack creates a distraction by streaking naked through the crowd, the Doctor and Rose slip into the hospital, and discover that the army has become involved because the caveman has been identified as a genuine Neanderthal.
Fearing that the Neanderthal will be abused by over-eager scientists, the Doctor and Rose bluff their way into the room and rescue him, with the help of a friendly nurse named Weronika who just wants the best for her unusual patient. While Weronika misdirects the pursuing soldiers, the Doctor and Rose get the Neanderthal out of the hospital and back to the TARDIS, where the translation circuits kick in and he identifies himself as Das. He claims to have followed one of Rose’s people, a man named Ka, into a strange tree back in his own time, where he found himself in a place of manufactured things and was then unexpectedly transported here to the 21st century.
Jack and the Doctor trace Das’ path through time and determine that he originated from 24 May, 29,185 BC. The Doctor promises to take Das back home, but as he sets the TARDIS in flight, Das begins to disintegrate into a glowing green light. The Doctor is forced to abort the flight; Das’ body has been irradiated with the energy from the dirty rip engine, and any further attempt to travel in Time will tear him apart. Frustrated by his inability to keep his promise, the Doctor takes Das back to Bromley, and orders Jack to stay with him and help Das to get a good start in his new life. The Doctor sets up Jack and Das with a flat and a bank account accessible via a psychic credit card, and he and Rose then travel back in Time to sort out the time travellers who are responsible for Das’ being here in the first place.
Back in Das’ era, a team of researchers is nearing the end of their stay in prehistoric times, but a married couple, Jacob and Lene, have just received bad news: Lene, whose life has already been extended for 387 years, is about to suffer incipient renal collapse and die. The news makes them feel wrong, so they use the combo packs built into in their nametags to dose themselves with neurochemicals that take away the bad feelings. Jacob returns to work, but begins to wonder why they haven’t yet returned home, and why some of his co-workers have failed to return from the Grey Door in the research base. When he asks the project head, Chantal Osterberg, she reminds him of the combo that will take away his feelings of anxiety -- and when he gives himself this combo, he forgets why his questions seemed so important.
The TARDIS materialises in a beautiful prehistoric forest, but as the Doctor and Rose explore, they spot a handsome young man wearing jeans and eating a baguette from a tin lunchbox. Surprised by their arrival, he flees at incredible speed, showing that he’s physically very fit. As the Doctor and Rose try to track him down, they find the half-eaten corpse of a woolly mammoth, and as the disturbed Doctor studies the strangely human tooth marks in the corpse, he and Rose hear movement and realise that the killer is still here. Loud music then blares across the clearing, and as the creature scurries off, the Doctor and Rose catch a glimpse of it; it appears to be a tall and gangly humanoid. The music is coming from two more blandly handsome newcomers, Tom and Jacob, who explain that they use these “stingers” to frighten off the indigenous animals whenever they visit the surface. Tom and Jacob assume that the Doctor and Rose are here to take them home, but otherwise show no curiosity about the newcomers -- or indeed any emotion of any kind.
Tom and Jacob lead the Doctor and Rose to a false tree that hinges up to reveal a hydraulic lift, which leads them to an underground village built entirely from wood. The inhabitants of the village are just as handsome and bland as Jacob and Tom -- with the exception of the senior zoo-tech T.P. Quilley, a loud and obnoxious “Refuser” dressed in outlandish clothing. Quilley is the only one who has noticed anything odd about the fact that their retrieval is nine days overdue, but nobody responds to his attempts to raise a fuss about it. The Doctor asks Rose to stick with Quilley and find out what she can; meanwhile, Jacob introduces the Doctor to Chantal, who assigns Lene to show him around. As they set off, the Doctor notices that Lene appears exhausted, but she simply uses combos from her pack to give her a fresh burst of energy and shows no concern or fear about the fact that she’s due to terminate soon. The Doctor tries to shock her by telling her to explain everything to him as if he’s a stranger with no idea what’s going on, but as he’d suspected, she sees nothing strange about this request. She explains that this village is an experimental observation post set up to study the early history of mankind; Chantal, whose intelligence has been enhanced to plus-810 level, chose to launch the experiment at the earliest point in human history, and if this mission succeeds, other observation posts will be established in different eras.
Meanwhile, Chantal receives a message from a being named “X-01” requesting food, and she thus sends Tina, one of the project’s typists, down to the Grey Door. Tina is unnerved that she’s been told to do something that’s unrelated to her job, and worried by the fact that a number of her co-workers seem to have vanished after visiting the Grey Door. However, a dose from her combo pack deals with her anxieties, and she cheerfully walks down to the Grey Door, where something yanks her inside and bites off her head.
In 21st-century Bromley, Jack is trying to teach Das how to fit in with homo sapiens. Some concepts Das grasps easily; he is particularly delighted by the discovery of fatty snack foods, and soon works out that, since the people of this time do not have to hunt for food, they have grown bored and invented many other things to occupy their time. However, in many ways, Das’ brain does not work quite the same way as a human being’s; for one thing, he is unable to lie, and can’t comprehend the concept of someone deliberately speaking untruths. Jack, bored with everyday life in Bromley, takes Das to the nightclubs of New York City, but while Das easily meets a woman who claims to like rough men, she makes her excuses and departs when he tells her that he is a Neanderthal who was transported from the past in a time machine.
Back in Osterberg Village, Quilley soon realises from Rose’s odd behaviour that she is not from his time. The Doctor joins them and explains to Rose that the researchers are from the Great Retrenchment, circa 436,000, when the Earth became collateral damage in a war between Kallix Grover and the Sine Wave Shrine of Shillitar. A magnetic wave missed its target and struck the Earth, shutting down all digital technology and cutting off the planet from its off-world colonies. The human race was forced to revert to purely analogue, mechanical technology, and they began to concentrate on the biological and chemical sciences; humans from this era have mapped out their anatomy so precisely that they could easily take a human body apart and put it back together with no ill effects. Most people from this era, apart from Refusers like Quilley who believe that raw human emotions enable them to savour life, use chemical blockers to regulate their emotions -- and a result, nobody ever feels anxious or worried, and nobody ever strives for anything other than what they already have.
The Doctor asks Rose to look around and try to find out more about the thing that killed the mammoth; on Quilley’s suggestion, she accompanies an observer named Reddy to visit the Neanderthal village on the surface. Meanwhile, Quilley leads the Doctor to the rip engine, which is steam-powered and even more dangerous than the Doctor had anticipated. It’s also operating at full capacity, and the power is being fed to another part of the compound. The Doctor follows the pipes to the Grey Door, where he and Quilley hear Tina apparently calling for help; however, when they unlock the door, something large, gangly and humanoid kicks it open, tosses out Tina’s skeleton and mimics her voice, asking if the newcomers are humans. Realising that the creature will eat them if it believes them to be inferior, the Doctor uses his sonic screwdriver to knock Quilley’s hat off his head without touching it, thus frightening the creature into retreating back behind the Grey Door. The Doctor and Quilley lock the door again, but then Chantal arrives, with a remote control linked to Jacob’s and Lene’s combo packs. Driven to a frenzy by the release of neural combos, Jacob and Lene attack the Doctor and Quilley and knock them out -- and Chantal then has them forget their strange behaviour and return to work while she investigates the Doctor.
Reddy is the young man whom the Doctor and Rose saw when they first arrived; he explains that he ran from them because he thought they were from the nearby human tribe, and these primitive humans, who have no control over their emotions, sometimes act strangely and use a thing called violence. Reddy claims that he wants to understand primitive behaviour, but he clearly has no idea where to start, and the irritated Rose eventually removes his nametag and tosses it away, telling him to experience primitive emotions for himself. Reddy, surprised that this had never occurred to him before, leads Rose to the Neanderthal camp, where he is known and accepted; in fact, one of the Neanderthal girls, Ka, regards him as her boyfriend. Rose tells the Neanderthals that Das is safe and well but will be unable to return to them, and they accept this and are happy for him. But just as Rose is starting to appreciate the Neanderthals’ carefree life, humans from the nearby tribe attack the camp, and when Rose tries to intervene, the humans capture her and drag her back to their caves.
The Doctor awakens to find that Chantal has given Quilley a combo pack and sent him back to work; she has also given the Doctor a combo pack, thus preventing him from feeling anxious as she operates on him and studies his alien biology. She explains that she knew the Doctor and Rose were lying about their intentions right away, but that she decided to let them wander about on their own so she could find out what they were up to -- unlike Das, who caused such a commotion when he broke into the village that Chantal simply transported him elsewhere in Time at random. However, the Doctor has learned too much about Chantal’s creations, the Hy-Bractors, and now she will have to deal with him. Chantal finishes her exploratory surgery and puts the Doctor back together, but he then gets an idea; it takes a while for it to arrive, but when it does, he realises that he’s just had the very good idea of overpowering Chantal, tying her up, and setting off to find Quilley. He does so and then runs out of ideas for a while, but seeing Rose’s jacket in Quilley’s shack reminds him that he should go looking for her.
Eventually, a technician named Tom finds and releases Chantal. Due to his combo pack, he asks few questions when she orders him to accompany her to the Grey Door; once there, she releases the Hy-Bractors, who devour Tom. Thanks to the Doctor’s interference, Chantal has decided to bring the schedule ahead, and she sends out her creations to devour the humans -- all of them except herself and the Doctor, who could still prove useful. Meanwhile, it finally occurs to the Doctor to remove his and Quilley’s combo packs, and while searching for an antidote, he discovers that the refills have run out -- which implies that Chantal no longer needs to keep her staff pacified. The Hy-Bractors then arrive and begin to eat the bewildered villagers, but the Doctor slaps Quilley until he’s angry enough to shake off the effects of the combo pack, and sends him to rescue the surviving villagers while he heads up to the surface to save the native humans and Neanderthals -- and Rose.
Rose awakens to find herself a captive of the cave people, who believe that they have rescued her from the Neanderthals, who are unlike them and therefore evil. Nan assumes that Rose was sent to trade and demands to know what her skills are; realising that they will turn on her if she fails to impress them, Rose offers to do the cave people’s nails. Impressed by her skills as a manicurist, Nan decides that Rose will make a good addition to the tribe, and announces that their two tribes will be joined by marriage. Rose protests until she gets a good look at Nan’s grandson, Tillun, the most fit and attractive boy she’s ever seen. Nevertheless, she decides that marriage is a step too far, and convinces Nan that she must appease her god Ooh-La-La by walking out alone to face the sun before her wedding. Tillun isn’t fooled and follows Rose into the woods, genuinely upset and unable to understand why she wouldn’t want to marry him, when he’s the king of the tribe and always gets what he wants. The Doctor then arrives, having used his psychic paper to tame a wild horse by convincing it that he is the god of the horses. He warns Rose of the danger posed by the Hy-Bractors, but when they try to warn the rest of the tribe, nobody will listen to the Doctor, since he isn’t one of them. Frustrated, Rose gives in and agrees to marry Tillun so that the tribe will accept her as one of them and heed her warning.
In 21st-century Bromley, Das is beginning to grasp the concept of lying, and he thus gets a job as a construction worker by claiming to be from Romania. He is enjoying his new life, without the worry of having to go out and hunt for food every day, and is beginning to settle in. Jack has been taking him out clubbing, and Das has met the most beautiful woman he’s encountered so far in this strange time, a woman whose “friends” call her Big Fat Anna-Marie. Das eventually proposes to Anna-Marie, much to her father’s delight, as he never thought that his daughter would find a match. Jack is satisfied and itching to move on, and is deeply relieved that he managed to prevent Das from hooking up with another woman they met briefly at a nightclub -- Rose’s mother.
In Osterberg Village, Quilley tries to explain the situation to the other villagers, but they’re too placid and serene to understand that their lives are in danger. Only Lene will listen to him, as her combo pack has run out and she’s beginning to become frightened. Jacob accompanies her and Quilley to the lift, and moments afterwards, the Hy-Bractors arrive. The other villagers, though terrified, have no idea how to respond to this unexpected situation and thus remain to be devoured. Quilley, Jacob and Lene escape to the surface, but one of the Hy-Bractors follows them.
Rose is officially wed to Tillun, thus becoming Rose Glathigacymcilliach. The tribe now listens to her warning and flees to safety in their caves before the Hy-Bractors arrive -- all except for Rose herself, who prepares to ride off with the Doctor to warn the Neanderthals. When the furious Tillun attacks the Doctor, accusing him of stealing his wife, the Doctor overpowers him and flees with Rose on his tamed horse. He and Rose now realise that the creature that killed the mammoth was a Hy-Bractor that Chantal had temporarily let out to acclimatise itself to its new world; however, they still have no idea why she’s breeding these monsters. They arrive at the Neanderthal camp too late; the Hy-Bractors have arrived and devoured most of the Neanderthals, leaving only a few alive to lure the Doctor and Rose into a trap. Chantal stuns them into submission with her stinger, and orders the Hy-Bractors to spare Rose -- unless the Doctor refuses to co-operate.
Back in Osterberg Village, Chantal explains to the Doctor and Rose that she has concluded that homo sapiens is perfectly adapted for survival as primitive hunters in a cold climate; however, when the Ice Age ended, humanity retained its hard-wired aggression and competitive nature, and spread across the world like a plague. Chantal thus became director of this project by killing off her rivals, and once she had returned to the dawn of human history, she bred an upgraded form of humanity and used the extra energy from the rip engine to accelerate their growth. Once the Hy-Bractors have been released into the world, they will devour all competing species, replace humanity and create a Utopia in Chantal’s image. To ensure that her project will succeed, she has surgically removed her empathy with other human beings, so the Doctor is unable to convince her that what she’s doing is wrong. Furthermore, while under the influence of his own combo pack, he told her that he had a working time machine of his own, and she intends to use it to spread her vision of Utopia across all time and space.
The Doctor refuses to help her -- until Chantal reveals that she’s surgically removed Rose’s head from her body. Rose is still alive, awake and aware, but if the Doctor refuses to co-operate, Chantal will not put Rose back together again. The Doctor reluctantly prepares to let Chantal into the TARDIS, but when Rose tries to step forward to stop her, a cabinet on the other side of the room clatters, and the Doctor realises that Rose still controls her body even though her head is no longer attached to it. He thus distracts Chantal by explaining the intricate technology involved in the TARDIS’ lock, while Rose works out what’s happened to her, gets over the shock, and steps out of the locker, distracting Chantal just long enough for the Doctor to overpowers her. Claiming that Rose’s trust in him is proof that evolution sometimes gets it right, the Doctor slaps a combo pack onto Chantal’s chest and gives her a dose of combo 199/87, leaving her completely unconcerned about the fact that the Doctor has just defeated her.
The Doctor then uses the equipment in the laboratory to force-cultivate a particular gene and splice it into some gut bacteria; he then leaves to disperse his concoction into the air, assuring Rose that he will return for her. Up on the surface, the Doctor’s spray spreads quickly -- and has an interesting effect. One of the Hy-Bractors catches Tillun searching for Rose, another finds the cowering Quilley, Jacob and Lene, and a third finds its way into the laboratory and advances on Rose. But Rose picks up her head from the table, points it at the Hy-Bractor, and spits out a sheet of fiery acid, blowing off its head -- as do Quilley and Tillun, on the surface.
The Doctor returns to the laboratory and assures Rose that this new ability will fade within minutes -- but in the meantime, Chantal has wandered off, vaguely aware that her plans have failed and intending to use the rip engine to leap ahead to the 21st century and start afresh. The Doctor and Rose arrive too late, and she ignores the Doctor’s warnings, steps into the time field, and is torn apart, just as Das nearly was earlier. Just as the Doctor had originally feared, the rip engine now becomes unstable, and the Doctor and Rose retreat to the TARDIS and escape moments before the rip engine explodes, wiping out the village of Osterberg. However, Rose’s head is still separated from her body, and the Doctor admits that he doesn’t know how to fix it.
The TARDIS materialises on the surface, where Tillun has found Quilley, Jacob and Lene. When the Doctor emerges, the furious Tillun spits at him, but fortunately his ability to spit fiery stomach acid has worn off, and he flees in terror when the headless Rose steps out of the TARDIS. The last of the Hy-Bractors then arrives, but the Doctor informs it that Chantal died after passing on instructions that the Hy-Bractor is no longer to eat human beings. Since the Hy-Bractor is still young, was told not to eat the Doctor and has been bred to be unfamiliar with the concept of lies, it accepts the Doctor’s claim and agrees to live in peace with the human beings.
Lene then reveals that she has the knowledge to reattach Rose’s head, but after doing so, she collapses and dies, her body finally wearing out. Jacob begs the Doctor to save her life, but there’s nothing the Doctor can do. Quilley shows genuine sympathy for Jacob’s loss, instead of the overblown and dramatic emotions he’s shown before, and as he comforts the stricken Jacob, he accepts the Doctor’s claim that they will be unable to return home and will have to make a new life for themselves with the cave people. The Doctor and Rose return to 2005 to pick up Jack, but stick around for Das’ wedding to Anna Marie O’Grady. Back in the past, Quilley marries Nan so that their two tribes may be united, and when he learns that some of the Neanderthals survived the Hy-Bractor attack, including Ka and Reddy, he asks Nan to accept them into the tribe as well. Nan agrees, albeit reluctantly, thus making the human race just that little bit more civilised.