The year is 1959, and the British and Americans are about to launch an experimental space plane into orbit from Winnerton Flats, a converted Georgian manor house and estate. Colonel Thomas Kneale will pilot the Waverider, having won the coin toss with Captain Davey O’Brien. Project director Edward Drakefell seems oddly tense as the launch approaches, but everything seems to go smoothly at first. However, there is an explosion upon re-entry, and as Kneale struggles to maintain control there is a second, even more devastating explosion. The Waverider crashes nearby, and as the press are ushered out, expatriate American reporter Rita Hawks hears the American General Crawhammer insisting that the Russians must have shot the Waverider down. But when radio contact is made with the surviving pilot, it isn’t Kneale -- it’s O’Brien...
The Doctor has been unable to confess to Ace that he found her dead body and that she doesn’t have long to live. After learning of Mel’s death, the Doctor accepts that he can’t shield Ace from danger forever, and conducts a thorough investigation into the circumstances of her death. Her body bears a tag from St Thomas’ Hospital, and a tattoo which reads “Ace + Jimmy”; the last thing she ate was a toffee apple; and she had sex before she died. Having narrowed down the date of her death, the Doctor “repairs” Ace’s torn jacket, slipping an electronic tracker onto it in the process, and takes her to London in 1959. The TARDIS materialises in the cellars of St Thomas’ Hospital, and the Doctor and Ace emerge to find that the hospital is deserted apart from American soldiers. They find a single patient covered by bedsheets and hooked up to complex life-support systems; according to his chart he’s named Davey O’Brien, and apparently belongs to the non-existent British Space Agency. The delirious O’Brien asks the Doctor if he’s Dumont-Smith come at last, but a nurse arrives and the Doctor and Ace must bluff their way out of the hospital and flee.
It’s been three weeks since the Waverider disaster, and Rita Hawks has started a media frenzy by printing Crawhammer’s accusations against the Russians. An anonymous tipster has started feeding her titbits indicating that Drakefell is involved in a conspiracy to hide the truth about the crash, and Drakefell has retreated to Winnerton Flats, where he is cracking under the pressure as his secretary, Sarah Eyles, watches in sympathy. Elsewhere in London, pensioner Arthur Baulstrode finds evidence of pests in his garden -- and is attacked by a swarm of giant ants when he investigates.
The Doctor has become intrigued by the mystery at the hospital, but Ace wants to explore. The Doctor gives her money and sends her on her way, aware that he’s taking a risk but knowing that her death is connected to the hospital in some way and hoping to keep her out of danger. But his plan to keep track of her backfires when she tears her jacket again -- and discovers the tracker which the Doctor has planted on her. Ace punches a car bonnet in a rage and storms off to London Zoo, where she tosses the tracker into the monkey cage. While there, she meets an American zookeeper named Jimmy who offers to give her first aid for her hand. Attracted to him and furious at the Doctor, she agrees to go out on a date with him after he drops off a package for a friend. But she’s unaware that she’s being watched...
The Doctor finds a solicitor named Miles Dumont-Smith in the phone book and breaks into his office -- where he is unexpectedly reunited with detective Cody McBride, whom he met during the Cyberman incident in 1942. McBride is shaken to encounter the Doctor again, and explains that Dumont-Smith’s wife hired him to investigate her husband’s infidelity. However, he and the Doctor find a sophisticated radio transmitter inside the man’s desk, suggesting that he may be a Soviet spy. The Doctor then discovers that the signal from Ace’s tracker is nowhere near their appointed rendezvous, and McBride drives him to the Zoo, where he finds the abandoned tracker and realises that Ace is in terrible danger.
The Doctor accompanies McBride back to his office, where he shows him the newspaper for the day after tomorrow and the article about the “unidentified” young girl’s death. McBride’s client then arrives, and the Doctor recognises her from a by-line in the paper; she’s not Mrs. Dumont-Smith at all, but Rita Hawks. Rita admits that she hired McBride on false pretences, having been tipped off by her informant that Dumont-Smith was a Russian secret agent involved in the cover-up of the Waverider crash. She’s surprised when the Doctor claims to have met the pilot, Davey O’Brien, in London; as far as she knows, the pilot was Colonel Kneale, and O’Brien is under house arrest at Winnerton Flats. She’s also been following a courier who has delivered packages from Dumont-Smith’s office to a small cottage in London, and when McBride develops her latest photos, he and the Doctor see that Ace is in the courier’s company.
Events are proceeding towards Ace’s death. The Doctor asks McBride to enlist official help, but their old partner Inspector Mullen isn’t pleased when they show up. He’s on bomb disposal duty, and as the Doctor tries to explain their situation, giant ants tunnel out from beneath the building where he’s working, and the vibrations set off the bomb. Mullen’s legs are shattered by the explosion, and must be amputated. Once again McBride and the Doctor have ruined Mullen’s life; when the army moved in to confiscate the army of Cybermen Mullen and McBride had found in the sewers, they tried to go public but were discredited. Mullen’s career never recovered -- and now the doctors are talking about fitting him with bionic legs, which he sees as the first step towards becoming a Cyberman himself.
Mullen considers committing suicide, but he and McBride find themselves laughing hysterically at the prim and proper nurse, and McBride vows to keep Mullen company and see him through this. Dr. Bill Hark promises that Mullen won’t be forced to submit to any procedure he doesn’t want, but Mullen and McBride have caused trouble for Hark’s work in the past, and he has other plans. Hark then contacts General Crawhammer, having found something intriguing -- the Doctor has checked himself out of the hospital, but has left behind some fascinating X-rays. Meanwhile, international tensions grow in the wake of the Waverider crash, as the Russians continue to deny responsibility and accuse the American government of using the test flight as cover to launch a spy satellite into orbit.
Unable to locate Ace, the Doctor gives Rita a message for McBride and goes to Winnerton Flats to question the other Davey O’Brien. He forces his way past his guards and contacts O’Brien, who covers for him, having been under house arrest for three weeks with no real explanation. The Doctor confirms that there’s another Davey O’Brien in hospital in London, to this O’Brien’s relief; the top brass have had him and Drakefell talking to a psychiatrist, but he was always sure that he’d heard his own voice on the radio. Drakefell arrives to arrest the Doctor, but the Doctor is starting to understand why Drakefell is suffering from such terrible guilt. Just as Drakefell is about to break and confess all, however, Crawhammer takes over, convinced that the Doctor is a Soviet spy. The Doctor tries to explain that the Russians aren’t involved, and that he knows why the rocket that came down is not the same one that went up, but when Hark contacts General Crawhammer to tell him about the Doctor’s X-rays, Crawhammer becomes certain that the Doctor is just what they’d always feared -- a Russian “augment”.
Rita tries to pass on the Doctor’s message to McBride, but McBride and Mullen have locked the nurses out of Mullen’s room and are drinking together. Unsure what the Doctor’s earlier talk of collapsing realities means, but understanding that a young girl is in danger, Rita follows their only lead to the cottage where she saw Ace with Dumont-Smith’s courier. Emily, the old lady who accepted the package from Jimmy, invites Rita into the cottage, but inside Rita feels momentarily dizzy and finds a paper with a bizarre headline which implies that the late King is still alive. When Rita tries to leave, the sweet old lady effortlessly restrains her until Dumont-Smith arrives. Dumont-Smith injects Rita with a knockout drug, but he has overestimated her people’s tolerance to such drugs and she is seriously disoriented during her interrogation -- which is observed by a shadowy third figure. In her confusion, she repeats what the Doctor told her about the walls of reality coming down, and Dumont-Smith and his superior conclude that their opposite numbers already know too much.
The Doctor is subjected to invasive medical tests and scheduled for vivisection, as Crawhammer is determined to prove that the Russians have their own augmentation project. Unwilling to stand by while a man is tortured to death, the Major Bill Collins helps the Doctor to escape. Disoriented by the drugs he’s been given, the Doctor leads the pursuing soldiers into the hedge maze to lose them -- and in the centre of the maze, he sees Drakefell unburdening himself to his secretary, Sarah Eyles. During the war, Drakefell was kidnapped from the Underground by the Cybermen, and although he escaped he was traumatised by the experience. When McBride and Mullen tried to go public about the discovery of Cybermen in the sewers, Drakefell investigated and learned about the Augmentation project, an attempt to adapt Cyber-technology to humans. Drakefell got himself assigned to the project and tried to sabotage it from within, but one night after a party in the lab beneath London Zoo he found a machine which he’d never seen before and which gave him horrible nightmares when he touched it. Drakefell had the machine sent into storage and transferred to the British Rocket Group, but the operation at the zoo was shut down and the equipment was all shipped out to Winnerton Flats. Trying to get rid of it forever, Drakefell planted it aboard the Waverider in place of the American spy satellite -- but something went terribly wrong. Now the wreckage has been brought to Winnerton, and Drakefell will once again be forced to face the nightmare machine, all the while knowing that his actions have pushed the world to the brink of war. The Doctor realises that someone else is listening in on Drakefell’s confession, but the other figure loses the Doctor in the hedge maze -- which should be impossible for a human, even considering the Doctor’s disorientation. The Doctor staggers back to O’Brien’s cottage and collapses.
Ace has spent the past day and a half with Jimmy. After delivering his friend’s package to the cottage, Jimmy took her back to his hut, where he lent her his bunk and slept on the floor. The next day, after a bout of drinking they impulsively get tattooed with each other’s names. They then return to the Zoo, where Jimmy buys Ace a toffee apple -- and this time, when they go back to his hut, neither sleeps on the floor. Eventually, however, Ace’s thoughts return to the Doctor, and when she decides to track him down, Jimmy’s mood turns ugly. He refuses to let her leave the hut, and when she tries to force her way past he locks her in, apparently under the impression that she’s a Commie spy because of the hammer-and-sickle badge on her jacket which she got from Captain Sorin.
Rita eventually shakes off the effects of the drug and breaks out of the cottage by digging through its thatch roof with a broken strut from her cot. It’s surprisingly dark outside, and she is nearly run down by a taxi which is driving with its lights off so as not to confuse the nocturnal wildlife. The driver offers her a lift without expecting money in return, and laughs off Rita’s claim to have been attacked by Russian agents; he is terribly condescending and patronising towards Americans, and claims that the Russians are their allies. Rita believes that the drugs are still disorienting her as the taxi driver whips her through streets full of traffic moving at breakneck speed without lights. The taxi delivers her to the address she requested -- but where she expected to find McBride’s office she finds a Chinese restaurant which has obviously been there for several years...
O’Brien hides the Doctor in his cottage, hoping to learn what’s been happening to him. As the Doctor recovers he and O’Brien note the strange flight patterns of birds over the nearby woods, and investigate to find a hidden aircraft hanger in the forest. Drakefell has dismissed the guards so he can confront his nightmare machine, acting on the orders of his psychiatrist -- the man who lost the Doctor in the hedge maze. The Doctor is beginning to guess his enemy’s identity, and suspects that the frost which Drakefell claims constantly covered the nightmare machine was in fact Vassar Dust, a by-product of time travel which put Drakefell in telepathic contact with the underlying reality beneath all space and time, traumatising him even further.
The Doctor, O’Brien and Drakefell enter the hangar to find that the space plane which crashed is a sleek ship which bears no resemblance to the rocket that went up. Inside, they find a dimensional stabiliser built into the ship’s controls, confirming the Doctor’s suspicion that this ship is from a different timeline. The other O’Brien was on a mission to drill through the walls of reality, but when he did so his ship was caught in the explosion of the Waverider from this universe. The Doctor suspects that Drakefell was not the only saboteur involved in that explosion, but that’s a problem for another time; the presence of the giant ants confirms that the barriers between the timelines are breaking down, and only this ship’s dimensional stabiliser can repair the damage.
Major Collins arrives as the Doctor attempts to remove the stabiliser, and is infuriated to see that the man he tried to help is now apparently sabotaging the Waverider again. As he tries to arrest the Doctor, however, commandos storm the hangar and attack Collins and his men. The attackers move like lightning and are apparently wearing bulletproof clothing, and when the Doctor electrifies the ship’s hull, the commandos begin to shell the ship, apparently willing to destroy it in order to prevent the British from examining it. Drakefell manages to flee with the dimensional stabiliser, but the Doctor inadvertently falls into the Waverider’s escape pod and is ejected to safety. As the Waverider explodes behind him he can do nothing but mull over his failure. He now knows that Drakefell’s nightmare machine was the lode-circuit of the time machine used by the Cybermen, which the Doctor last saw in the possession of a master of strategy who played the British and Nazis off against each other and even outwitted the Doctor. He has identified his enemy, but too late to save Ace...
McBride returns to his office and finds the message which Rita left. Time has been running out for Ace while McBride has been drinking with Mullen. McBride returns to the Zoo to look for a lead, and hears Ace calling for help; however, Jimmy catches him trying to rescue her, and as they fight, McBride recognises him as James Dean, the movie star who should be dead. The fight ends with Ace manacled to the wall and McBride trapped in a cage of the Augmentation Project’s rejected experiments -- cybernetically augmented apes whose implants are powered, like dodgem cars, from the electrical grid in the cage’s ceiling. Jimmy’s boss then enters to confront Ace, and she recognises him as George Limb, the frail old man she met in 1942 who’d seemed so kind until she learned he was selling British secrets to the Nazis. Limb admits to Ace that he ordered to Jimmy keep her occupied until he was ready, and that Jimmy is now torn between his feelings for Ace and his loyalty to Limb. Nevertheless, and despite profuse apologies, Limb shoots Ace in the head and orders Jimmy to dump the body in the Thames.
Limb leaves, failing to notice McBride shouting protests over the clamour from the ape cage. McBride lashes out at Jimmy, and Jimmy, racked with guilt, snaps and turns the power in the cage up to maximum. The agonised apes tear into each other, pummelling McBride unmercifully, but Limb returns and switches the power off, and McBride slips out unnoticed. He calls in the police, but due to the presence of the augmented apes there is an official cover-up of the incident. Crawhammer is convinced that the experiments he’d ordered destroyed were maintained by a cell of Russian agents -- and he’s also convinced that the commandos who attacked his men at Winnerton Flats were Russian. Even though the commandos were armed with stun weapons and none of Collins’ men were seriously injured, the incident has driven international tensions even higher; the British and American governments are demanding apologies and reassurances, but Premier Khrushchev continues to deny responsibility and accuses the governments of fabricating the incidents themselves.
The next day, the Doctor and McBride bury Ace in the grave where the Doctor found her in the future. The Doctor blames himself and is about to walk away from the whole mess, but McBride cuts through his web of self-recrimination and temporal paradox and reminds him that he owes it to Ace to bring her killer to justice. The Doctor agrees, and they start by looking for the missing Rita Hawks at the cottage where she took the pictures of Ace and Jimmy. The walls of reality are extremely thin here now, however, and a swarm of giant ants breaks into the house and attacks as they investigate. The Doctor and McBride set the house on fire, but a police constable trying to arrest them panics when he sees the ants and calls in the army -- and the Doctor is once again taken captive.
Dr. Hark takes the Doctor back to St Thomas’ Hospital, where he is confined on a ward with Mullen and this timeline’s O’Brien. The Doctor tries to explain that he’s an alien, but Hark is convinced that the Doctor is the product of a Russian cybernetic augmentation programme and is terrified by the implication that their research is more advanced. Mullen has been sedated, but the Doctor palms one of his sleeping pills and slips it into his guard’s coffee. Once the guard is asleep, the Doctor will attempt to escape through the furnace shaft -- but O’Brien can hear sounds on the floor above, incoherent cries of distress which deeply unnerve him.
Rita is trapped in a bizarre London where Americans are regarded with pity and distaste, people and traffic move like lightning, the war ended two or three years earlier, and the Russians and the British are allies. Her editor recognises her and gives her a press pass to a reception at the Savoy, and Rita is thus able to get one good’s night sleep; however, she flees when she hears a woman with a disturbingly familiar voice berating the management for letting someone else into her room. On the street outside, Rita meets her old friend Stella, and is horrified when Stella steps up against the wall and plugs two thin wires into the back of her head -- a procedure which doesn’t strike anyone else as unusual at all.
Drakefell tells his psychiatrist, Dr Hopkins, all about the incident at the hanger and gives him the dimensional stabiliser for safekeeping. What he doesn’t realise is that “Hopkins” is in fact George Limb, who subsequently contacts Dumont-Smith and berates him for letting his men blow up the craft and lose its technology. Irritated by the Russian’s short-sightedness, Limb decides not to tell Dumont-Smith that he has the surviving component -- but Dumont-Smith and Emily later break into Drakefell’s home and force the terrified scientist to tell them what he did with it. Rita’s interrogation has given them the impression that their enemies know the truth, and when Dumont-Smith learns that Limb lied about having the stabiliser, he concludes that Limb has betrayed them.
As soon as the Doctor’s guard falls asleep he climbs up the furnace shaft to the floor above, where he finds the other timeline’s O’Brien. This version of O’Brien has been cybernetically augmented, but the technology used is far beyond Hark’s understanding, and his clumsy attempts to repair the damage from the crash have left O’Brien struggling to move unwieldy bionic legs and dying as his organic body isn’t provided with the processed energy it requires to survive. The alternate O’Brien admits that his country’s Prime Minister ordered that a permanent breach be made between the dimensions, but before he can explain more, the fully human O’Brien arrives to warn the Doctor that they’re searching for him. McBride then turns up to rescue them, but they’re forced to leave the weakened Mullen and the cybernetic O’Brien behind. Outside, the Doctor is startled to learn that McBride is working with Jimmy Dean, Sarah Eyles -- and George Limb, who claims that he needs the Doctor’s help to prevent a war.
McBride remains with Drakefell and with Sarah, Limb’s grand-niece, who genuinely believes Limb to be a good and kind man. The Doctor, Limb and Jimmy head for the Houses of Parliament to look for someone who will listen to the truth before war is declared. Limb admits that he’s been travelling in the Cybermen’s time machine, which didn’t disintegrate as the Doctor had hoped it would. He experimented with changing history, saving James Dean on one occasion, and on another helping the British government to harvest the Cybermen’s technology and win the war in 1943. However, he was never able to control his travels fully, and on his last journey, the machine broke down completely and catapulted him back in Time while itself remaining in 1959. Limb is due to catch up with it in a couple of days. He tried to repair the damaged component by infiltrating the Augmentation Project, but was forced to leave it behind one night when a party of scientists nearly caught him in the lab. When he returned the next day, Drakefell had encountered and been traumatised by the lode-circuit, and had sent it into storage.
Limb is now stranded, but he knows his destiny. He has seen many versions of his own future, and despite all of his efforts to change things, the outcome is always the same -- he is doomed to fall victim to the Cyber-conversion process. In order to prevent this, he’s been selling the secrets of the Augmentation project to the Russians via Dumont-Smith in order to provoke an arms race and a war which will definitively change his future. However, when he saw Ace at London Zoo, he realised that there was another alternative, and he thus lured her into a trap, killed her and planted clues on her body to lure the Doctor here and now and force him to help. Limb believes that the Doctor can teach him how to change his future and travel safely in time, and that he can then prevent himself from killing Ace -- but the furious Doctor informs him that time travel doesn’t work like that. Travellers can only change other timelines, not their own; Limb will never escape his future as a Cyberman, and even if he saves Ace, somewhere in the multiplicity of timelines she will always be dead, his victim. Worse, by meddling in the course of history and creating alternate timelines which should never have exited, Limb has caused the barriers between realities to break down, and now that they’re interacting with each other the Time Vortex is on the point of collapse.
Rita spends an uncomfortable night in a park, and then learns that the Prime Minister is due to address the people of London. A familiar face informs the crowds that a threat to their way of life will soon be dealt with, and planes like nothing Rita has ever seen before fly through a rift which has appeared in the sky. In the other Britain, PM Macmillan makes a radio address denouncing the recent Soviet aggression, but just as it seems that he’s about to declare war, a dimensional rift opens in the sky above London and the other timeline’s planes fly through. Limb realises too late what the Doctor had guessed when he learned that the cyber-O’Brien was deliberately trying to tunnel through realities. Dumont-Smith was not a Soviet agent at all, but a spy from another timeline, and now that he knows Limb has been holding out on him they have brought their invasion plans forward. Britain is being invaded by the cyber-augmented British, and the alternate timeline’s Prime Minister is George Limb.
As the alternate timeline’s commandos seize control of London, the Doctor and Limb return to St Thomas’ Hospital, where Crawhammer, Collins and their men have set up post. As the commandos storm the hospital, McBride and the human O’Brien arrive with the augmented apes from London Zoo, and the Doctor has little choice but to activate them and send them out to do battle. In the chaos, Crawhammer finally accepts the Doctor’s claims and agrees to a plan which should end the invasion. Limb and Jimmy escape, taking an augmented gorilla as their bodyguard; however, the Doctor was expecting a betrayal and slipped the tracker he’d earlier planted on Ace into the lining of Limb’s coat. McBride asks the Doctor to send back the TARDIS so he can rescue Mullen, and the Doctor agrees to do so. McBride takes Hark hostage and tries to rescue Mullen, but they are captured by commandos under the command of Captain Frank Williams who have fought their way past the apes. O’Brien tries to rescue his counterpart, but he’s forgotten that the cybernetic O’Brien is on the invaders’ side, and is captured when his counterpart calls out for help. Meanwhile, Crawhammer and his men fight their way back to Winnerton Flats, along with the terrified Drakefell, and once there Crawhammer contacts the alternate PM and threatens to launch nuclear missiles at the rift unless the commandos retreat.
The Doctor traces Limb and Jimmy back to the ruins of Emily’s cottage, where he finds Dumont-Smith’s dimensional stabiliser and transfers himself to the alternate timeline’s Ministry of Augmentation. There, he finds Rita, who is looking desperately for a way home and has slipped in with the people seeking free augmentation in order to fit in with society. The entire world begins to quake as the barriers between timelines break down further, but the Doctor and Rita successfully locate Limb, who is confronting his alternate self. The PM explains that cyber-augmentation has resulted in a utopia where people never age and die, and that the planet is becoming overcrowded, hence their invasion of the other timeline. When Crawhammer contacts him with his ultimatum, the PM refuses to withdraw, calling what he knows to be the Doctor’s bluff. Limb agrees with his counterpart’s reasoning and shoots him, intending to augment himself and take the PM’s place -- but the bullets have no effect. The PM has gone all the way and become fully cybernetic, yet another variation of Limb’s apparently inescapable destiny. Horrified, Limb unleashes his gorilla bodyguard on the PM, and he and Jimmy escape as the gorilla and the PM tear each other apart.
McBride and his friends are confronted by the furious Captain Williams, who has lost several men to the augmented apes and is appalled and horrified by the clumsy surgery conducted upon O’Brien’s counterpart. As Hark tries to defend his actions, a dimensional rift cracks open and a swarm of giant ants spills out onto the street, tearing Hark apart. McBride, Mullen and the human O’Brien are unexpectedly rescued when the rift opens further -- and a fifty-foot-tall Ace emerges from the ants’ timeline. The giant Ace drives off the augmented commandos, and when the PM is destroyed in the other timeline, Williams gives the order to retreat. Unfortunately, as the cyber-British retreat, Drakefell snaps, and Crawhammer reacts too late, shooting and killing him but not before he’s launched the nuclear missiles through the closing rift.
The Doctor locates the PM’s personal dimensional stabiliser, and he and Rita cross back into their own timeline in the cemetery where Ace is buried. Limb has finally caught up with his own time machine, and he now has a dimensional stabiliser with which to repair it -- and cause even more damage in his attempt to avert his future. The Doctor informs Jimmy that Ace was pregnant when she died, and the horrified Jimmy finally sees Limb for what he is and turns his gun on him. Limb manages to activate the time machine’s force field, shutting everybody else out, and as he tries to dematerialise, Jimmy retreats -- and then returns, barrelling into the cemetery in his car, crashing into the time machine and dying in a horrific car wreck just as he was destined to do. Limb’s life is saved by the force field, but he is gravely injured and the time machine is beyond repair. Now knowing that he can’t escape his destiny, Limb asks the Doctor for help, and the Doctor hands him Jimmy’s gun. Rita retreats sadly from the cemetery as a shot rings out.
Later, the survivors celebrate their victory at Mama’s Bar -- which McBride thought had been destroyed by a German bomb during the Blitz. The dimensions are realigning and inconsistencies are smoothing themselves out, and the giant Ace is shrinking as her size becomes relative to this dimension. The Doctor decides not to tell her that her counterpart was shot and killed, and also decides not to disillusion Sarah Eyles, who mourns the loss of her great-uncle George. Mullen accepts that he will spend the rest of his life with artificial legs, and the Doctor and Ace decide to remain and celebrate Christmas before setting off on their travels once more.