Over the centuries, a mysterious albino appears before the females of an American family, until 1972, when he finally locates Loretta van Cheaden, the one who will be his Ini-Ma. In 1993, he collects Loretta and several other homeless people from Los Angeles and transports them to Micronesia, where they prepare for his ascension. Reporters Shelley Kurtzmann and Damien Braun arrive to investigate rumours of a mysterious temple in the jungle, and learn too late that it was planted there to lure them into the albino’s clutches; they are to play an important role in his plans. But the albino is being followed. In Auckland, a telepath named Mike Dudley finds him and reports in to his superiors, but then a darkness closes in around Dudley -- and when it vanishes, so does he.

Meanwhile, strangers have come to Halcham, a small village in the Peak District. The newcomers generally keep to themselves, but whenever someone in the village needs help the teens are there almost at once, quickly and efficiently repairing the damage or lending a helping hand. Sebastian Malvern, the scion of the family which founded the town’s rope-making business, has vouched for the newcomers, and the villagers gradually come to accept them. Despite wishing them well, Reverend Cummings suspects that the strange Irish twins who seem to be in charge of the “family” are trying to atone for dark deeds in their past -- but even he is surprised when one day he brushes against the Irish man and finds his skin hard and cold, almost like plastic. These are the twins who caused the Doctor such trouble in the past, and the three teens are the victims of SenéNet, their minds erased and reprogrammed to serve as the twins’ slaves. Ciara and Cellian have repented and wish to help the teens recover, but they need help -- and late in December 1993, Ciara dreams for the first time in years, of the Doctor returning to Earth.

Mel discovers that not only has the Doctor failed to return the VW he rented in Australia, he’s added a sun roof and racing stripes. The Doctor reluctantly agrees to pay the rental agency for the car, but instead of arriving in late-1960s Australia, the TARDIS materialises in Whitby in 1993. There, the Doctor spots a newspaper story which sends him to the small Norfolk town of Great Rokeby in a state of some irritation. It appears that his former travelling companion Evelyn Smythe, who first left Earth with the Doctor in March 2000, has used her knowledge of the future to win a contest by guessing a famous chef’s chocolate-cake recipe five years before it’s made public. However, Evelyn is rather irritated with the Doctor herself, as he dropped her off on Earth over a decade before her departure without the means to pay her way. As her younger self is still teaching in Nottingham, Evelyn can’t go home and must keep a low profile, using knowledge of the future to make just enough money to get by, without drawing attention to herself or changing history.

Meanwhile, in Paris, former UNIT captain Therése Gavalle answers a mysterious invitation and is taken to the headquarters of the Network, a secret organisation located far beneath the city. Although most who work for the Network believe it to be a branch of the French government, it’s run by a foppish, upper-class Englishman who has named himself John Doe to cover the fact that he has no memory of his past. Doe invites Gavalle to join his team, but only after she signs up does she learn that she’s committed herself to work for the all-powerful secret criminal organisation known as the Magnate. For some reason the Magnate has taken an interest in her, possibly due to her alien encounter in 1980; she vanished on Réunion, holding off a hostile alien while her team members escaped, only to reappear two years later with no memory of the missing time. Doe reveals that the Network has access to a group of ESPnets, powerful psychics who run errands for them under the belief that they’re working for the UN. Mike Dudley was one of their agents, and due to his disappearance the Network needs a replacement; Gavalle is to travel to England with two assassins, Ms de Meanour and Ms Feasance, to secure him. In the meantime, Doe continues to pursue his private agenda -- revenge against the Third Doctor and Brigadier Lethbridge-Stewart, whom Doe blames for the half-remembered accident which caused his memory loss.

Trey Korte, Mel’s American friend, has spent four years using his newly discovered psi talents to help out UNIT and C-19, while searching for some trace of his lover Joe Hampton. One day he confronts an alien who has taken on the form of a human entrepreneur in order to steal cloned human tissue, and while Hope-Unwin agrees to leave quietly, he reads Trey’s mind before going and points out that Trey himself knows he will never succeed in his quest. As Trey tries to come to terms with this, he finds himself under attack, hunted telepathically by the powers behind the Magnate. He manages to get to his friend Bob Lines and warn him, but then must send himself into a coma to avoid detection. However, he’s too late; Gavalle and the assassins find him, bribe an odious junior administrator named Tim Hall to let them into the hospital, and then kill Hall and kidnap Trey. Bob, who is due to retire today, tries to research the Magnate first, but soon realises that he’s out of his depth. He thus uses his signal beacon to call in his old friend the Doctor.

The Doctor tells Mel that he needed someone he could trust on Earth to keep an eye on things for him, but while speaking with Evelyn, Mel realises how deeply hurt she is by the Doctor’s actions. Mel confronts the Doctor, and catches him studying news clippings which Evelyn has been collecting for him -- reports regarding the Irish twins, who caused Mel such distress when she first met the Doctor. The Doctor admits that he asked Evelyn to watch out for them, as he can’t afford to obsess over one problem on Earth and lose sight of the millions of other worlds that need his help. Despite the trauma she suffered at the twins’ hands, Mel insists upon confronting them with the Doctor, and Evelyn also insists upon accompanying them both.

Elsewhere, former Vice-Marshal Charles Dickinson is living alone in a retirement home, having outlived his wife and both of his children -- or so he thinks. But one day, his friend Woody Ashburn unexpectedly claims to have spent time working on black ops projects -- and that his memories were erased and he was sent here when he learned too much about an organisation called the Magnate. Charles would dismiss this as senile paranoia, but for the fact that Woody also claims to have seen Charles’ son Justin alive in France, even though Charles had received word that Justin was killed in action while working with UNIT in 1978. Before he can reveal more, Woody dies of an apparent heart attack, but Charles finds an empty syringe near the body and then finds an envelope addressed to him in Woody’s handwriting. In his letter, Woody claims that Justin is alive but not entirely well and is holed up at the Network, a black ops unit set up by the French government; and that Sir John Sudbury, head of C-19, suffered his fatal “heart attack” when he tried to expose the Network’s corruption.

As the Doctor and his companions set off, the Doctor receives Bob Lines’ call regarding Trey’s kidnapping, and agrees to investigate. Mel suggests using the Internet to search for evidence on the Magnate; as this is 1993 and the Internet is only beginning to become public, Evelyn suggests visiting the nearby University of Sheffield. It’s closed when they arrive, and they must book rooms at the nearby inn for the night. After another argument between the Doctor and Evelyn, Mel questions the Doctor again, and he admits that he’d always regarded Evelyn as a different kind of companion, almost his intellectual equal; when she decided to stop travelling with him, it hurt him more than he would admit. Mel suspects that the TARDIS picked up on this and deliberately dropped Evelyn off years too early, to punish her for hurting the Doctor.

Charles Dickinson is still unsure whether to believe Woody’s claims, until the duty nurse at the home is unexpectedly replaced by a newcomer who claims that no patient by the name of Woody Ashburn ever existed. When Charles investigates, he finds that Woody’s room has become a file storage room -- but there’s still a stain on the linoleum where he recalls spilling his tea, and when he examines the files he finds his own hospital records, complete with a note about the fatal heart attack he is due to suffer in five days’ time. Charles promptly walks out of the home before any of the new “staff” can stop him, and takes a taxi to the railway station, heading for Paris.

Gavalle and the assassins take Trey to Malvern Hall to rest before their return to Paris, but Malvern insists that the Irish twins take care of Trey for the night. Gavalle is upset, but realises that Malvern is too powerful for her to oppose. During the night, she wakes to hear a strange humming noise, and catches Malvern communicating with the alien which she encountered on Réunion; however, the alien once again erases her memory, and she wakes the next morning without recalling the incident. Meanwhile, Trey wakes to find himself a prisoner of the Irish twins once again, and is particularly furious when he sees Joe, who doesn’t seem to recognise Trey at all. As he can’t read the twins’ minds, it’s up to them to convince him that they really did change once Trey and the Doctor killed the Managing Director of SenéNet and banished the Nestene intelligence which had been dominating their actions. Ever since then, they’ve had to live with the guilt of what they’ve done, and they seek to atone for their crimes; but to do that they must save the world, and for that, they need Trey’s help.

Meanwhile, in Micronesia, Shelley and Damien watch as the albino’s followers prepare the temple for his ascension. Damien realises that the idols set up around the perimeter are all from different religions, and when he recognises one as a statue of Kahless the Klingon he realises that the temple is just window dressing for the main show. But it gets rather hard for him and Shelley to dismiss the forthcoming ceremony as rubbish when Loretta, who now calls herself Ini-Ma, speaks to them telepathically...

The Doctor decides to divide his forces; he will continue on to Halcham to confront the twins, while Evelyn and Mel remain in Sheffield to research the Magnate. However, another argument breaks out when he presumes to believe that Evelyn will lend him her car without being asked, and by the time she calms down, he’s stolen it. Mel and Evelyn continue on to the University library, where Mel realises that Evelyn’s former dean -- the one who was trying to revoke her tenure in the year 2000 before she left with the Doctor -- currently works at this University. While Mel tries to track down the Magnate, Evelyn intends to dig up some dirt on the dean for use when she returns to her own time. Rather upset, Mel confronts Evelyn about her behaviour towards the Doctor, and Evelyn admits that she began to travel with him because she’d recently been divorced from a husband she still loved, and saw her travels as a means of escape. She eventually came to terms with her loss and realised that she was ready to start her life again -- but the Doctor dropped her off in the wrong time, and her life’s been on hold ever since.

Using her knowledge of the future, Mel rewires the library’s Internet connection and designs her own search engine to locate information on the Magnate, but she finds herself blocked at every turn; somehow, the Magnate can protect itself against techniques which are even slightly advanced for 1993, and all she’s done is alert the Magnate to her presence. John Doe is warned of the danger, and he contacts Gavalle and orders her to send the assassins to Sheffield while she returns to Paris with Trey. The two assassins catch Mel and Evelyn in the library, but their superhuman strength proves to be their downfall when a mistimed blow smashes through a stack support and brings the entire library roof down on the assassins’ heads. Mel and Evelyn flee back to the inn, assuming that the assassins have been crushed to death.

Gavalle brings Trey to the Network, much to Doe’s satisfaction; he believes that the Doctor was responsible for the interference in Sheffield, and is sure that he will have his revenge. All he can remember is looking for his friend Sarah-Jane in the Doctor’s laboratory, and finding instead a machine which hurt him in some way. But already his plans are in jeopardy; Trey is not in a coma as Gavalle had believed, and he makes contact with his fellow ESPnets and reveals the truth to them. Meanwhile, Charles Dickinson arrives in Paris, and, following the coded instructions in Woody’s letter, finds his way into the Network. The head of security, Maurice Devin, is intrigued when Charles claims to have come looking for his son, who may be suffering from amnesia after some sort of accident. Devin thus informs John Doe of Charles’ arrival, but when Doe arrives, Charles doesn’t recognise him. In a fit of pique, Doe orders him killed, but as Devin marches Charles out the Network they pass the room where the ESPnets are held -- and Charles recognises one of them as his son Justin...

The Doctor arrives in Halcham, but the villagers close ranks, unwilling to betray their friends to a stranger. However, Ciara herself arrives and invites the Doctor to their home near the cave to talk. Although he’s not entirely convinced by the twins’ claims to seek absolution, the Doctor agrees to speak to their benefactor, Sebastian Malvern. Malvern reveals that he’s one of the most powerful psychics on Earth; on a scale on which the Doctor would be 6 or 7, and Trey would be a 12, Malvern is a 50. He is also Kyto-Ma, the link which binds the alien Cylox named Tko-Ma to Earth. On the same psychic scale, Tko-Ma and his brother Lai-Ma would be the equivalent of level 1000, powerful enough to manipulate and destroy whole galaxies on a whim -- as indeed they once did. They were punished for their crimes and exiled to another dimension, but Lai-Ma escaped by bonding himself to a human psychic, his Ini-Ma. Tko-Ma bound himself to Malvern in order to locate his brother; he is the real Magnate, using the forces of the Network to track down Lai-Ma, and the rumours of a vast criminal organisation were set about to obscure the truth. Malvern, however, is not so naive as to believe that Tko-Ma will meekly return to his imprisonment once Lai-Ma has been recaptured. So far, Malvern has managed to hide his true agenda from Tko-Ma; he seeks to stop the Cylox from destroying the world between them, and to find redemption for foolishly wishing his parents dead after a bitter argument, a mistake no psychic as powerful as himself should ever make. But he needs the Doctor’s help, particularly now that he knows Gavalle has encountered Tko-Ma before. Tko-Ma must have planted a psychic power in her brain -- something which he will no doubt trigger at a most inconvenient time.

The Doctor agrees to help, but then he thinks of Mel and Evelyn, and Malvern realises that the assassins were sent to kill them. The Doctor calls Mel at the inn, and to his relief he gets through to her... just as the assassins return, having killed the paramedics who dug them out of the wreckage. As the assassins prepare to kill Mel and Evelyn, Malvern takes the Doctor to the cave for improved psychic reception, and contacts Trey in Paris. Together, Malvern and the ESPnets generate a teleport storm, and transport Mel and Evelyn to the cave... unfortunately, along with the assassins. The Irish twins use the guns built into their arms to hold off the assassins, but Malvern is having trouble keeping all of this from Tko-Ma, and they’re running out of time. It’s New Year’s Eve, and soon Lai-Ma will begin to draw the power of the Cylox realm into himself and use it to take over the dreamscape of every living being on Earth.

The Doctor, reasoning that Lai-Ma and Tko-Ma need each other to support their own power, tells Malvern to send him to the Cylox realm. In the meantime, the ESPnets combine forces to bleed the power of the Cylox realm away into Paris. Justin telepathically warns his father of the danger, and Charles helps him to hold the door of the ESPnets’ chamber closed while the Network begins to collapse around them. Tko-Ma, sensing danger, triggers his fail-safe, and Gavalle comes entirely under his control. Devin tries to flee, but Gavalle uses her powers to throw him into the path of an oncoming subway train, and then generates her own teleport storm to get to the cave and stop Malvern. Doe realises that he’s been manipulated all along, and follows her, seeking revenge and answers.

The Doctor finds the missing Mike Dudley in the Cylox realm, surviving by sheer force of will. After convincing Dudley that they’re on the same side, the Doctor uses bluster and threats to irritate Tko-Ma into appearing before him. Angered by the Doctor’s intrusion, Tko-Ma reveals that he and Lai-Ma had their powers docked as part of their punishment, which is why they need human psychics to do their work on Earth. The Doctor realises that Tko-Ma only wants to get Lai-Ma back to this prison realm so he can be reborn on Earth himself; the Cylox are merely children, playing a game to see who can destroy the Earth first. But while the Doctor has been distracting Tko-Ma, the ESPnets have been drawing off most of his realm’s power; soon it will be gone, and he will vanish with it. Tko-Ma can only survive if he agrees to let the Doctor preserve a fraction of the astral plane’s power, just enough to keep him trapped. He has no choice but to agree or die, and the Doctor thus traps him in an infinite loop of space. Now he and Dudley must find a way back to Earth to stop Lai-Ma...

Gavalle and Doe arrive in Halcham, where Gavalle shoots Malvern in the leg, trying to break his concentration and strand the Doctor. Before she can shoot him again, however, Tko-Ma warns her of the change in circumstances, and she returns to Paris, intending to force the ESPnets to send her to her master. In the ruins of the Network, she shoots Charles Dickinson in the head and opens the door of the ESPnets’ chamber, only to be vapourised when the Cylox energy pours out; however, to the ESPnets’ surprise, the energy vanishes before it can destroy the world. Back in Halcham, Cellian shoots Ms Feasance as she tries to follow Gavalle, but Ms de Meanour is too close to Ciara when she tries to shoot, and due to the assassin’s superhuman strength the blast blows off Ciara’s arm even as it kills Ms de Meanour. Ciara dies, and Cellian dies with her. Malvern passes out from blood loss, and the teleport storm closes up, apparently stranding the Doctor in the Cylox realm. Doe, confused and enraged, threatens to kill them all for manipulating him, but the villagers then arrive to investigate, and pub owner Gary Rudge shoots and kills Doe before he can kill Evelyn.

In the Cylox realm, the Doctor realises that the power which was flowing into Paris has been redirected towards Lai-Ma, who was trying to draw the Cylox realm into himself but will now receive far more energy than he’d expected. The Doctor and Dudley follow the power flow and emerge in the temple in Micronesia, where Lai-Ma had intended to force Shelley and Damien to broadcast his ascension to the world so all could witness his rise to power. Now he’s burning with the energy from the Cylox realm, and it may cost the Doctor his life to trap Lai-Ma in the infinite loop of Cylox space. But then Ini-Ma reveals herself to be no ordinary human, but the Cylox’s jailer, her personality passed down through Loretta’s bloodline. The Doctor gives her the loop and retreats, but realises too late that Ini-Ma has passed judgement on the criminals and does not intend to re-imprison them. Instead, she casts herself and Lai-Ma into the loop with Tko-Ma, and the loop overloads with energy and explodes, killing all three of them.

Later, Trey and Dudley address an emergency meeting of the UN security council to announce that the ESPnets will no longer be used as pawns; instead, they will leave the governments of Earth to their own petty squabbles, while acting independently to protect the world from external threats. The Doctor chooses not to intervene, as his mistakes have already cost the lives of one set of powerful children -- and of “John Doe”, whose mind was destroyed when he foolishly tried to fiddle about with the Doctor’s IRIS machine following the incident with the spiders. “Doe” was never really part of UNIT, just a well-meaning hanger-on who wanted to fit in, and as the Doctor never really liked him that much he didn’t bother to find out whether he’d recovered afterwards. A great many deaths could have been avoided if only the Doctor had made more of an effort to be nicer to poor Jeremy. Malvern continues to work with the teens, trying to break down the alien blocks on their memories, but Trey realises that he’ll have to forget Joe and move on with his life... unaware that Joe, whose mind is still blocked to Trey, still does remember all of their time together. The Doctor has resolved the twins’ legacy as best he can, and at Mel’s urging, he agrees to return Evelyn home... but at Evelyn’s request, they’ll take the scenic route.