Hordes of UFO spotters descend upon the village of Greyfrith when strange lights are spotted in the winter sky. One such hopeful, Arnold Knight, is attacked by a robot in the fields outside town, and is struck by a car when he flees onto the icy road. The driver, local schoolteacher Debbie Castle, is unable to flag anyone down; the only car to pass by, a black VW, carries a strange young couple who refuse to help her. She sets off on foot in search of help, and finds it at a local farmhouse with a police box in the yard. The farm’s owner, a Doctor, allows her to use his phone to call an ambulance, and offers her a cup of tea to relax after seeing Arnold off. She has to get back to her sullen husband, Barry, but, seeing that the Doctor plays chess, she invites him to her school’s chess club meet on Tuesday. However, as Tuesday draws to a close the club’s opponents cancel due to bad weather, and Debbie sees the strange couple from the VW, Rum and Thélash, standing by the gate and watching the children leave. They seem amused when Debbie confronts them, and tell her that they are the Hunters -- which she assumes is their surname, rather than a description. When the Doctor shows up, the Hunters grow pale and depart hurriedly. Their mission to find the Last One is difficult enough with the UFO spotters roaming the countryside, and their associate, who has chosen the name “Mr Gibson” to blend in on Earth -- for what good it will do -- isn’t making things any easier. If he learns that the Doctor is present, things will get fraught. Mr Gibson and the Doctor have issues.
When the Doctor learns that the chess club’s opponents aren’t coming, he sets up eleven boards and plays chess against Debbie and all ten children simultaneously. Debbie finds the Doctor to be much more pleasant company than Barry, and, trying to think of topics to keep him talking, happens to mention that her student Miranda has an odd birth defect... two perfectly formed hearts, one on each side of the body. The Doctor is fascinated, particularly when he realises that Miranda is letting him win so he can make a clean sweep -- and even more so when he hears the children discussing the accident and learns that Arnold claimed a robot attacked him. The Doctor asks Debbie to tell him all she knows, but first waits with Miranda for her mother to arrive. He discusses the UFO sightings and the possibility of life on other worlds with her as they wait, and Miranda proves to be a bright and innocent young girl... whose breath doesn’t condense in the cold air. The Doctor then visits the pub with Debbie, where he admits that he doesn’t remember anything about his life before waking on a railway carriage many years ago. Barry finds them together, and jealously challenges the Doctor to a snooker game. The Doctor allows him to win by sinking all of the balls, including the cue ball, in a single shot; humiliated, Barry forbids Debbie from ever seeing the Doctor again. However, she decides to read up on chess strategies, hoping to challenge the Doctor to a rematch one day. And in one book she sees the Doctor, just as he appears now... in a photograph taken in Stalingrad in 1951.
Intrigued by what he’s learned so far, the Doctor visits the hospital to speak to Arnold and check Miranda’s medical charts. Unfortunately, Mr Gibson has learned of the Doctor’s presence, and he orders the Hunters to dispose of Arnold before the Doctor intervenes. Unaware that they are already too late, they disintegrate Arnold in his hospital bed. When the Doctor learns of Arnold’s “disappearance”, he confronts the Hunters, who believe that he knows who they are and is just toying with them. As the Doctor leaves, Rum reveals to Thélash that he slipped a mini-nuke into the Doctor’s coat pocket; if he starts to pose a real threat, they can dispose of him at any time. But the Doctor also picked Rum’s pocket, stealing his communicator. That night, the Doctor contacts Debbie, asking to borrow her car so he can track down some aliens. She thinks he’s joking until he uses Rum’s communicator to trace the Hunters to the local lovers’ lane, where he parks next to the black VW and leads Debbie to a field where the Hunters have just summoned a flying saucer. The Doctor confronts the new arrivals, Prefect Zevron of the Klade and his deputy Sallak, realising that they are here for Miranda...
Zevron realises that the Doctor, their race’s greatest enemy, genuinely doesn’t remember having met them before; he may be from a period before Last Contact. Zevron therefore invites him aboard the saucer to discuss Miranda, telling the Hunters that their services will no longer be required. A servant takes the Doctor’s and Debbie’s coats and shows them to a waiting room, where Zevron and Sallak explain that Miranda is the last scion of a corrupt intergalactic empire; her people were brutal tyrants who set in motion events which led to the devastation of the timelines. Under Zevron’s leadership, the corrupt factions of the Senate finally put aside their diferences and united against the Imperial Family. The Family executed Zevron’s mother, leaving him to raise his younger brother Ferran by himself; Zevron has thus declared a blood feud on them, and Miranda, the last of the Family, must die by his hand. The Doctor, appalled, refuses to help Zevron kill an innocent ten-year-old girl -- and Sallak thus slaps a mindeater onto the Doctor’s head before he can react. The mindeater drains out what memories he has, including the memory of Miranda’s pediatric chart, and her home address...
Zevron and Sallak board hover-discs which draw their power from the saucer, and depart assuming that the now mindless Doctor will soon die. Instead, he recovers, and he and Debbie escape. Outside, they find Barry, who has brought another woman to the lovers’ lane and is furious to find his wife there with another man; but before he can do anything about it, the Hunters’ VW transforms itself into the killer robot which attacked Arnold earlier. This is Mr Gibson, a sentient mechanoid who blames the Doctor for the destruction of his world. (In fact, although the Doctor can’t remember it, all he did was free Mr Gibson’s slaves, and Mr Gibson himself panicked and set off the bomb which destroyed his own palace and queen.) As Barry’s girlfriend flees in her own car, the Doctor, Barry and Debbie pile into Debbie’s car and drive off, with Mr Gibson in pursuit; however, when Barry learns that the robot’s associates are trying to kill a young girl, he insists that they save her first. The Doctor tricks Mr Gibson into swerving off the icy roads and over a steep hill, and then drives the car after him, leaping out at the last moment while the car collides with Mr Gibson and destroys him.
Miranda’s “parents” are in fact a bodyguard and nurse from the Imperial palace, who couldn’t bear to let the rebels murder a two-month-old child. They realise too late that they have been located. Kim Dawkins drugs Miranda so she’ll sleep thorugh whatever is to come, and flees with her. Sallak kills her husband, but Kim gets as far as the Doctor and the Castles before Zevron and Sallak catch up and kill her. As Zevron prepares to stab Miranda through the hearts, the Doctor tries to reason with him; how can he build a lasting universal peace on the murder of an innocent child? As Zevron hesitates, Barry attacks him, grabs his gun and shoots him in the head, but as he dies Zevron slaps a mindeater onto Barry’s head. Rum and Thélash, watching from the saucer, decide that enough’s enough and detonate the mini-nuke in the Doctor’s coat pocket... unaware until it’s too late that the Doctor left his coat in the waiting room. The saucer’s destruction robs Sallak’s hover-disc of power, and he falls to earth, pinned beneath the disc, an easy capture for the police when they finally arrive.
In the aftermath, Sallak pleads guilty to avoid a trial, and is locked up in a prison for the criminally insane. Barry remains in a coma for reasons unknown to 20th-century medicine. The Doctor adopts Miranda, and vows to give her every opportunity to make her way in the world; thus, as the 1980s march on, he becomes a freelance business consultant, and makes millions by restructuring companies without creating redundancies. Unfortunately, he makes a bit of a name for himself, and eventually, Sallak reads about him in the newspaper and learns where he can be found. He immediately breaks out, along with his cellmate Joel, and sets up base in Joel’s former home, an abandoned council block known to the locals as the Tower. There, Sallak builds a device which uses static electricity to let him communicate across time. Zevron’s eighteen-year-old brother Ferran arrives in response, and tells Sallak that the uneasy truce between the factions will soon break down into civil war. Sallak is needed to ensure that the Klade reign supreme... but before they return, there’s a blood feud to take care of.
Miranda is nearly sixteen years old, and has blossomed into quite a beauty. She’s starting to take an interest in sex, though her interest is more intellectual than hormonal, as the Doctor has taught her how to control her body’s autonomous systems. Her friend Dinah is going out with Alex, whose friend Bob shows an interest in Miranda; curious, Miranda agrees to go on a date with him, to a party at Dinah’s home. She returns home to find the Doctor working on a five-dimensional equation, and helps him to solve it, unaware that it’s not an intellectual puzzle; she had fainted earlier, at her swim meet, but doesn’t realise that it’s because she sensed something travelling through Time nearby. The Doctor is trying to locate him, but his work becomes academic when he receives a phone call from Sallak. He and Ferran have gone to the hospital and woken Barry Castle just so he can see who’s killing him, and they have also kidnapped Debbie. If the Doctor wants to see her alive again, he’ll come to the Tower.
The Doctor tries to break into the Tower with a suitcase-sized device he invented to open locks with sound waves, but he is captured and brought before Ferran. Ferran and Sallak have brought in reinforcements and technology from their time zone, including a device which restructures matter on a molecular level, and an Interrogator. The Doctor resists the Interrogator for a while, but Ferran conducts the second session personally and proves too strong for him. The Doctor touches Ferran’s mind and senses him to be a decent man at heart, though corrupted by the hatred of those around him. Ferran, however, won’t listen to him, and he locks the Doctor up with Debbie and sets off to kill Miranda. Joel and his lover Kirst, who now realise that they’re part of something they really don’t want to be involved in, question the Doctor and eventually agree to help him when he offers them a million pounds, tax-free. They show him and Debbie to the restructuring unit, which Joel demonstrates by transforming a couple of bricks into a pile of red roses. The Doctor sets it to overload and flees with Debbie, Joel and Kirst as the transforming wave washes down the Tower after them. Ferran’s guards are too surprised to run, and are transformed, along with the Tower, into a mountain of red roses in the middle of the urban wasteland. However, Sallak escapes, blaming himself for the disaster; he knew how dangerous the Doctor could be, but still left him alive so he could gloat. He won’t make that mistake again.
Ferran tracks Miranda down at the swimming pools, but although he manages to get a good look at her he is unable to get her alone. He retreats, telling himself that he doesn’t want to make a public scene; hee’s always pictured his battle with the Last One as being more mythic, more apocalyptic, and simply killing her unexpectedly would be an anticlimax. Dinah, quite taken by the Aryan-beautiful Ferran, invites him to her party, but he leaves early and lurks outside, still telling himself that it’s not the right time. Miranda takes Bob out to the garden and allows him to kiss her, but feels nothing except a sense of having power over him. The other partygoers disperse, leaving Miranda, Bob and Dinah to spend the night in the house. Miranda decides that she’s overanalysing her own reactions, and decides to slip into Bob’s bed and let whatever happens, happen. But Bob isn’t in his bed; he’s in Dinah’s. As is Dinah. Furious, Miranda storms out of the house, but before Ferran can make his move, the Doctor drives up and takes Miranda home with him. However, he doesn’t tell her about the incident at the Tower; he has never told her anything about her past, wanting her to live a normal life.
The next morning, the Doctor drives Miranda to school, and then lets Debbie talk him into reporting his “stalkers” to the police. However, Miranda walks away from school after seeing Bob there, and meets Ferran outside -- and accepts his offer to skive off for a drink. Ferran takes her to a pub and tries to poison her drink, but his arrogant attitude gets them kicked out before she can drink it. Miranda, feeling somewhat vulnerable, finds that she can relax around Ferran and tell him what’s troubling her. As they leave the pub she stumbles and nearly falls in front of a speeding car, but Ferran automatically pulls her back to the curb... where they kiss. Miranda takes him home, but before they can go much further, the Doctor and Debbie return. The moment is lost, and Ferran pulls a knife on Miranda and tells her everything. Her race destroyed the Universe, draining whole galaxies of energy, shattering the timelines and leaving Ferran’s people with advanced technology but no resources with which to use it. He has seen the records of history in the Librarinth on the Needle, and knows that there is no mention of her after this year. But he doesn’t want to kill her -- he has fallen in love with her, and he wants her to return with him to the future, and rule by his side.
Miranda is stunned, and confronts the Doctor, who is forced to admit that it’s all true. But he insists that she doesn’t have to listen to Ferran; she can and must make her own destiny. It’s too much for her to take, and she tries to flee, but Ferran will have none of it; however, as he tries to drag her back to his side, the Doctor taps his recall bracelet and sends him back to his own time. Sallak then breaks in and holds them all at gunpoint, but this time he chooses to shoot the Doctor first, and is unprepared when Miranda attacks and overpowers him. She tries to hold him off, but he tells her that she’s evil through and through; if she lets him live, he will never stop hunting her. So she shoots him. The police arrive, summoned by the Doctor’s security alarms, and the Doctor, stunned, tells Miranda to go while she still can. As she flees, the Doctor turns himself in, claiming that he shot Sallak in self-defense. His claim is accepted, but by the time it’s all sorted out, Miranda has gone and the Doctor doesn’t know where she is...
Three years pass before they meet again. On the night that the Berlin Wall falls, Miranda is in India, sleeping with a fellow tourist. He will later go on to direct an autobiographical film depicting the most significant events of his life, and this film will survive in one form or another until Ferran’s time... and thus, when Miranda steps out onto the balcony the next morning, she is transmatted aboard a flying saucer and taken into Earth orbit. Ferran is no longer the young, fit man she remembers; twenty years have passed for him, and he’s spent them in the Librarinth, seeking Miranda and the other secrets of the past. His four-kilometre-long flagship, the Supremacy, isn’t actually a creation of his people, but a relic of a past time which may since have been erased from history. It crashed on the Needle some time ago, and his people are still learning its secrets; but soon he feels certain they will be able to build a fleet of similar ships and unite the warring factions of his time. His deputy and lover, Cate, seems to believe that only Ferran can prevent the ruined future from falling into anarchy, but Miranda knows that Ferran is just going to repeat the same acts his brother called atrocities when the Family was responsible for them...
The Doctor and Debbie learn of the UFO sighting in India, and intend to investigate -- but as the Doctor sets off to collect her, he buys petrol with his credit card, thus leaving a record of his location at this point in time. When Ferran shows Miranda how to use the Supremacy’s telepathic controls, she finds the records relating to the Doctor, and surreptitiously sends him a telepathic message explaining what’s happened. The Supremacy will be stuck in Earth orbit for three days while its systems conduct minor repairs; the Doctor has that long to get to her. Instead of going to India, he and Debbie therefore go to Florida, to hitch a ride on the space shuttle Atlantis. They slip through the cracks in the launch procedure routine and use the sonic suitcase to board the shuttle through a hatch which it is supposedly impossible to close from the inside. Once in flight, they reveal their presence to the crew as a fait accompli, and before the stunned astronauts can react, their shuttle arrives over India and the Supremacy is revealed in orbit. The mission objective changes instantly.
Miranda has the genetic codes necessary to enter restricted areas of the Librarinth and access all the secrets of her people’s past. This is why Ferran returned for her; he sees her only as property, just like Cate, whose name is short for dupli-Cate. Cate is a replica of Miranda, whom Ferran created just to impose his will on her. He has planted pain-inductors in all of his subjects to ensure their submission, for the strong always conquer the weak. Miranda, taking her father’s teachings to heart, insists that the Universe does not work that way, and Cate, believing her, snaps and attacks Ferran. He uses a pain inducer to punish her, but is then called to the flight deck to deal with an emergency, and gives the inducer to Miranda so she can have a taste of power. Instead, she asks Cate to help her escape, and Cate agrees to do so. Meanwhile, Ferran arrives on the flight deck to learn that Atlantis is approaching, and that the Doctor is demanding Miranda’s release. Ferran just laughs; the shuttle couldn’t scratch the Supremacy even if it rammed directly into it, and the computer will respond only to Ferran’s voice print. The Doctor therefore mimics Ferran’s voice over the radio and orders the Supremacy to shut down all but essential life support systems for twenty minutes, thus allowing the Atlantis to dock safely. Ferran, furious, sets off to kill the Doctor himself. Everyone in his time knows the legends of the Doctor, who kidnapped innocents, turned them into monsters and terrorists, and brought darkness to the Universe. Now Ferran will meet him face-to-face, and win.
Miranda’s plan to steal a saucer goes awry when the Doctor’s command shuts down power to the travel tubes, stranding her and Cate in an unexplored region of the Supremacy. There, they meet escaped slaves Graltor and Tarvin, who are surprised to meet the legendary Last One and even more surprised when she offers to help them escape. Cate doesn’t want to throw her lot in with mere slaves, but Miranda, irritated, points out that she too is a slave, and uses the pain inducer to prove her point. But the power loss has affected the pain inducer as well. If none of the inducers work, then the slaves can turn on their guards at last -- and Cate knows that many of the guards would join them willingly. Miranda changes her plan; instead of escaping, they will take over the Supremacy.
The Atlantis docks with the Supremacy, and the Doctor sets off with Debbie and Delta Force specialist Mather. They are separated from Mather when a bulkhead slams shut between them, and continue on alone -- but Ferran has set a trap for them at Miranda’s quarters, and Debbie is electrocuted when she tries to open the door. The infuriated Doctor attacks Ferran, proving Ferran’s point; this is all the Universe comes down to in the end. Ferran beats the Doctor nearly to death, or so he thinks until Cate arrives and announces that he has in fact finished the job. Strangely disappointed by the ease of it, Ferran return to the bridge, only to find a rebellion well underway. With Mather’s help, the rebels capture most of the ship, except for the flight deck and engine room, but Ferran’s response is to switch off life support everywhere else. Cate tries and fails to stop him -- but then the Doctor and Miranda burst in, and before Ferran realises what’s happening, the Doctor again mimics his voice and transfers control of the ship to himself and Miranda. Ferran simply can’t comprehend that Cate lied to him; once again the legendary Doctor has returned from the dead, and even the Doctor’s adopted daughter has started a revolution in less than ten minutes. But Ferran has been raised to seek revenge; it’s in his blood, and he transmats himself to the engine room, refusing to accept defeat.
The Doctor and Miranda go to the engine room to find Mather and Tarkin trying to break in, but they’re saved the effort when an elderly man in his mid-twenties opens the door and staggers out. When the engineers tried to surrender, Ferran uncoupled the time engines, releasing time spillage which killed all of the engineers and will soon destroy the Supremacy. By tonight the Earth will be a desert; by tomorrow the sun will be a red giant. The Doctor and Miranda may or may not be immune to the effect, but nevertheless they enter the engine room, where they find Ferran dressed in a protective suit and operating the controls. While the Doctor enters the engines’ central sphere to repair the damage, Miranda tries to convince Ferran that none of this is necessary. She knows him well enough to know that he hasn’t appointed a successor who might have challenged him for power, and without Ferran and the Supremacy, his people will be overrun by their enemies. He’s about to destroy everything he says he’s trying to protect, but this doesn’t have to end with one of them dead. There are other ways.
The Doctor subconsciously identifies the equipment in the sphere, and while conducting repairs he orders the engines to shut themselves down three days in the past, thus giving himself the time he needs to follow Miranda into orbit. As time shuffles about him, he catches glimpses of his future -- a swarm of wasps, Mr Saldaamir, violin music in the heart of a thunderstorm, a planet named Albert, a robot with flashing lights on its domed head and a camera eye-stalk... Finally, the Doctor completes his work, and emerges to find that Miranda and Ferran have come to an understanding. They address the assembled crew, who are now all equals -- except for Miranda. She is the supreme ruler of the Universe, and thus she has the power to declare that there will be no more rulers. There will be anarchy, and everyone will be free. No-one will be forced to fight beside them, but if they choose to do so, they can stand united against the evils of their own time, and make a better future together.
The Doctor forgives Ferran as best he can for Debbie’s death; after all, the Doctor is himself responsible for the death of Ferran’s brother, and they have to draw a line before they destroy each other and all else besides. Miranda asks the Doctor to come to the future with her, or to let her search the ship’s archives for some mention of “Fitz” or the Doctor and his police box. He turns down her offers; he knows she is capable of handling her new role by herself, and he’s so close to his appointment with Fitz that it would feel like cheating to learn the answer in advance. He returns to the Atlantis with Mather, and they watch as the Ship -- no longer named Supremacy -- returns to a future amongst the stars. The Doctor knows he’ll be doing the same one day soon.