Aboetta Cigetrais, the young housekeeper at Ashton Court, receives word that her father, whom she left in good health four months ago, has been struck down by a fever. Her employer, Mr. Malahyde, is sorry to see her go, and though she promises to return he seems to know something she doesn’t. Outside Ashton Court’s inner wall it is unseasonably bright for February, and Captain Bryant and Lieutenant Collins are waiting to escort Aboetta home to Totterdown, but the strain of guard duty seems to have worn them down, as they appear noticeably older than when Aboetta first arrived. They must cross Bristol by foot, but as soon as they’re out of sight of the Clifton Suspension Bridge they are attacked by a swarm of Wildren, the subhuman cannibals which inhabit the ruins of the city. Bryant and Collins are killed, but just as the Wildren corner Aboetta, a strange blue box materialises behind her and the Wildren scatter in terror.
The Doctor, Anji and Fitz emerge from the TARDIS to find themselves in the post-apocalyptic ruins of Bristol, facing a young woman with a gun who seems surprised by Anji’s skin colour and Fitz’s leather jacket. The yearometer identified this as 2003, but Aboetta claims that the year is 151, proving that time is still out of joint following the Siberian incident. Still wary of the new arrivals, Aboetta nevertheless knows they will all be safer if they stick together, and the Doctor thus agrees to accompany her to Totterdown. However, he’s doing so in order to investigate the existence of this alternate timeline; too many alternate histories are jockeying to fill the same position in reality, and the Time Vortex is threatening to collapse.
Aboetta leads the Doctor and his companions to the fortified settlement at Totterdown, where her lover Robin Larkspar opens the gates to let them in. As the suspicious Chief Elder, Morgan Foster, questions the strangers, Aboetta is reunited with Robin -- and is shocked by the change in him, as he is significantly older than he was when she left. Disturbed, she rushes home only to find that her father has been dead for days. Robin demands to know why she’s been gone for so long without word, and when Morgan arrives with the Doctor and his friends to confirm whether they did save Aboetta’s life, he confirms what Robin is telling her. She believes it is February in the year 151, but according to both Morgan and Robin, it is October of the year 160, and Aboetta has been gone for ten years.
Shaken, Aboetta confirms that the Doctor and his friends saved her from the Wildren and leaves to think things over. Morgan agrees to give the newcomers the run of the town for the day, but demands that they meet him at the pub at eight bells to explain themselves properly. Anji and Fitz decide to wait out the time at the pub, realising that Anji’s skin colour is attracting unwanted attention. At the pub, they are served soup, bread and vegetables, but no meat -- and they realise that they’ve seen no birds or animals anywhere since arriving.
As Aboetta tries to come to terms with her long absence, she meets another visitor to the town, the priest Father Gottlieb. Gottlieb claims to be visiting the town’s priest, Father Cluny, to pay his respects to her father, but he seems too interested in her time at Ashton Court, and she suspects that he has ulterior motives for asking. The Doctor also questions Aboetta about Ashton Court, and though his attitude seems kind enough, she senses that he poses a threat of some kind. As the Doctor sets off for his meeting with Foster, Aboetta retreats to the home of her old friend Evelyn -- now a much older friend -- but Robin tracks her down and demands to know what’s happened to her. Unsure how she feels, and realising that Robin is also confused and hurt, she accompanies him to his home, where they make love. However, she is dissatisfied with the older Robin’s performance, and when he falls asleep she realises there is nothing to keep her in Totterdown. She will return to Ashton Court.
At the pub, the Doctor, Anji and Fitz are questioned by Foster, Cluny and Gottlieb. The Doctor tries to evade any questions about his origins and directs the conversation to the topic of Ashton Court, but Gottlieb provokes Father Cluny by suggesting that whatever affected Aboetta may be related to the Cleansing. Talk of such things is forbidden, and when the Doctor tries to learn more, Foster decides to have him and his friends locked up and expelled from the town at dawn. However, their guard drinks himself into a stupor and Aboetta releases them, seeking help to return to Ashton Court. Gottlieb also arrives and offers to help them escape, but the Doctor is disturbed when Gottlieb kills a Watchkeeper in order to cover their flight. Aboetta is even more upset when she realises too late that there’s no way to secure the river gate from the outside. Gottlieb insists that they continue their flight, and Aboetta is forced to leave the river gate open, leaving the settlement defenceless.
Once they’re clear of the town, the Doctor inquires again about the Cleansing, and learns that the Earth was struck by a global catastrophe that wiped out 95 percent of the human race. The survivors eventually determined that Time itself had accelerated, causing forty years to pass in mere seconds. All adults and most animals withered and aged, children grew to adulthood almost at once, and the babies who found themselves in adult bodies became capable only of breeding and feeding; their descendants are the Wilde Kinder, or Wildren, subhuman cannibals little better than animals. The Doctor notes that since the Cleansing occurred in the old year 1843 and 160 years have passed since then, this should be the year 2003 -- but if another 40 years had passed all at once during the Cleansing, the yearometer should have registered this as being the year 2043. Time only accelerated along some of its dimensions, not all... which implies that the effect may have been deliberate.
The travellers make camp for the night once clear of the town, but when Fitz sleeps he has an unpleasant nightmare of the Doctor and Anji stamping out infinite realities and destroying countless souls. The next morning, he finds himself disturbed when the Doctor speaks of trying to “fix” this reality. When Anji tries to discuss their next move with Fitz, she is surprised by his hostile reaction, but he’s starting to wonder what makes their reality “right” and this one “wrong.” Don’t the people of this timeline have a right to exist?
The Doctor suspects that Aboetta’s employer is the key to explaining the mystery, but when they arrive at Ashton Court, Aboetta enters without acknowledging her companions and the gate guards drive them away. Frustrated, the Doctor agrees to join forces with Gottlieb, who admits that he and his associates have been planning a raid on Ashton Court for some time. As he leads the Doctor, Anji and Fitz to a fortified inn in the heart of Bristol, Gottlieb explains that the world turned to religion to explain the Cleansing; in the aftermath of the disaster, people concluded that God had restored the human race to a state of innocence, and thus they restarted the calendar from the date of the Cleansing. However, Gottlieb can’t believe that a rational God would slaughter so indiscriminately. The Doctor, meanwhile, notes the existence of the Clifton Suspension Bridge, which shouldn’t have been completed until the 1860s, indicating that history diverged significantly at some point before the Cleansing.
While crossing Queen Square, the party is attacked by a swarm of Wildren, and the Doctor and Fitz are separated from Anji and Gottlieb. Gottlieb does not hesitate to kill the attacking cannibals, and he and Anji escape via the canal and reach the inn. There, Anji is appalled to learn that Gottlieb’s associates are outlaws banned from the “civilised” communities for eating human meat. Gottlieb admits that he used false credentials to enter Totterdown in order to meet Aboetta and question her about Ashton Court; he has sought answers about his world all his life, and came to Bristol upon hearing rumours of a man named Malahyde who guarded a precious secret. He believes this Malahyde may be the descendant of the man who invented the Malahyde Process for manufacturing steel, a science which revolutionised world industry before Year Nought -- and which Anji has never heard of.
When Aboetta passes through the inner gate into the grounds of Ashton Court, she finds that the weather inside is still like that of February, and that the door she left open over a day ago is still ajar. Malahyde is delighted to see her back, but realises that he will finally have to explain himself, as he always knew he would when he first hired a housekeeper. He admits that Time moves more slowly than normal in the grounds of Ashton Court, and that although he seems to be in his early forties, he was in fact born before the Cleansing. He leads Aboetta to the cellar, which she was always forbidden from entering before, and shows her a strange machine which glows with an eerie green light; this is the Utopian Engine, and it’s responsible for the world in which they live today.
In 1831, Jared Malahyde was a young man with aspirations of being a poet, but all that changed after a brief encounter on the Downs with the famous architect Isambard Kingdom Brunel. Soon after they had parted company Malahyde was suddenly transported to the Eternium, the home of a species called the Eternines who claimed to be the pinnacle of human evolution. The Eternines claimed that in Malahyde’s time, humanity was entering a crucial period of history which would determine their future; either they would evolve into the Eternines or descend into destructive savagery. In order to ensure that history unfolded as it should, the Eternines needed an agent in the era to construct a machine that would let them travel back in Time and guide humanity to its bright, worthy future.
Malahyde’s body merged with an Eternine named Watchlar, who subsequently directed him through telepathic commands and occasionally took full possession of him. Under Watchlar’s guidance, Malahyde entered a partnership with Brunel and developed a new process for manufacturing steel which made them both rich. Brunel was able to construct his dream projects, the SS Great Britain and the Clifton Suspension Bridge, while Malahyde constructed the Utopian Engine. After twelve long years of work, research and setbacks, the Engine was finally completed, and Watchlar took full possession of Malahyde to activate it -- but when Malahyde woke, Watchlar had gone from his mind, and the Cleansing had occurred.
Malahyde soon realised what had happened, and discovered that his estate was now affected by an anomaly which caused Time to flow differently in the vicinity of the Utopian Engine. He built the inner wall to hide this fact from the outside world, and hired a series of guards, each of whom believes they were hired by the son of the man who hired their predecessors. Ever since the Cleansing -- which, for him, occurred only five years ago -- he has lived on the estate, guarding the Utopian Engine in the hope that one day Watchlar would return and help put things right. Perhaps it may even be possible for the Engine to roll back Time and make it so that none of this tragedy ever happened.
In the hour or so that it’s taken Malahyde to tell his story, over a day has passed outside. Gottlieb has convinced the outlaws of Bristol that Malahyde is hoarding powers which should be shared by them all, and the outlaws thus agree to attack the main gate, drawing the guards away while Anji and Gottlieb scale the outer wall and break in. What Anji doesn’t yet know is that the Doctor and Fitz also survived the Wildren attack -- and that while fleeing they encountered Robin Larkspar, who still loves Aboetta and abandoned his post in Totterdown to follow her and take her back home. The Doctor and Fitz take Robin to the TARDIS, where the Doctor disconnects the time element so he can make a short hop in space but not time; hopefully they will arrive in Ashton Court, rather than yet another alternate reality.
Gottlieb and Anji break into Ashton Court, and Gottlieb shoots out the lock on the inner gate to find that on the other side of the wall it’s still day, not night. Gottlieb holds Malahyde at gunpoint and demands answers, and Malahyde shows them the Utopian Engine but insists that he has no idea how it works. The TARDIS then materialises, and Robin emerges to take Aboetta back home -- but she’s made her decision, and Robin is stunned when she insists that she’s staying here with Malahyde. In the confusion, the obsessed Gottlieb tries to force answers out of Malahyde by operating the Utopian Engine himself, and before the Doctor can fix the damage, Gottlieb and Anji are swept up in a temporal rift and presumably cast out of reality altogether -- into the wild storm of the damaged Time Vortex, where the Doctor knows they’ll die in agony.
The Doctor insists upon leaving at once, and Fitz forces Robin to accept that Aboetta no longer wants him. The Doctor takes Robin back to Totterdown, leaving Aboetta and Malahyde to their isolation -- but it’s been broken once, and Aboetta fears that it may be broken again. She and Malahyde are now closer than employer and housekeeper, and Aboetta admits to that she stayed because she’s fallen in love with Malahyde. They make love in the master bedroom, but at the height of their passion, Aboetta experiences a vision of Watchlar.
Fitz finds himself deeply disturbed by Robin’s loss, which has brought home just how human he is. He thus sees Robin off in Totterdown, and as the Doctor tries to usher him back to the TARDIS, he points out that this version of reality has no pollution or overpopulation problems, and suggests that a Community such as Totterdown represents the triumph of the human spirit over even such adversity as the Cleansing. He thus refuses to help the Doctor wipe out this version of reality and insists upon remaining to prove his point. The Doctor doesn’t have time to argue, and reluctantly abandons Fitz to his principles -- warning him that if this reality ceases to exist, Fitz will be cast free into the Time Vortex to suffer the same fate as Anji.
As the TARDIS heads back to 19 July 1843, the day of the Cleansing, the Doctor discovers the real reason for Fitz’s change of heart. Every book published after the mid-19th century has vanished from the TARDIS library. Unable to handle the conflicting timelines jostling for position, the Vortex is trying to reconcile the contradictions; the Cleansing’s timeline felt more real to Fitz because his vulnerable biodata was adjusting to compensate for its existence. Back in Totterdown, Fitz finds his memories of the Doctor, Anji and the TARDIS fading away and being replaced by memories of a life in Totterdown with his best friend Robin. Within a day, Robin and Morgan Foster believe that Fitz has lived in Totterdown his entire life, and Fitz has forgotten all about the TARDIS.
Anji and Gottlieb are not in fact dead yet, but they’re stranded on a desolate beach near a faintly glowing green ocean, and there’s no sign of life anywhere. Gottlieb now accepts that he was foolish to meddle with something as powerful as the Utopian Engine, but understanding has come too late; he and Anji are stranded on a dead world, perhaps in a dead universe, with no hope of rescue.
The TARDIS materialises in Bristol on 19 July 1843, which should be the date the SS Great Britain was launched. However, in this history it’s been sailing for five years, and the Clifton Suspension Bridge is already complete. The Doctor makes his way to Ashton Court, where he finds Brunel trying to get past an intransigent servant, George, to speak with Malahyde on matters of business. The Doctor bluffs George into believing that Malahyde may be ill, and he and Brunel enter the manor house and find their way to the cellars just as Malahyde, fully possessed by Watchlar, activates the Utopian Engine. The Doctor and Brunel struggle with him, and the Doctor casts Malahyde into the energy field around the Engine, knocking him out. The Doctor then deactivates the Engine, but when he and Brunel emerge from the cellars they find George lying dead, his body a desiccated husk. Malahyde didn’t recognise the Doctor in Year 160 because he was possessed by Watchlar the first time they met; despite the Doctor’s efforts, this is still the world of the Cleansing.
The Doctor explains the situation to the horrified Brunel as they make their way through city streets littered with aged corpses. Presumably they were protected by proximity to the Engine, as its operator would have been. Brunel finally accepts the truth of things when he and the Doctor meet the terrified Emily Riverston, a four-year-old girl of Brunel’s acquaintance who is now in the body of a 44-year-old woman. The Doctor gets her to a nearby house and puts her to bed, and Brunel vows to help the Doctor ensure that this terrible event never happens.
Brunel recalls his first brief meeting with Malahyde on the Downs, and the Doctor pilots the TARDIS back to 22 October 1831 and tries to intercept the young poet. Malahyde ignores the odd stranger’s warnings and is caught up in the Eternines’ snare, and the Doctor has no choice but to pilot the TARDIS through the closing dimensional rift in pursuit. In the Eternium, he pulls Malahyde into the TARDIS before Watchlar can merge with him. As they flee in the TARDIS, the Doctor explains to Malahyde that this is not humanity’s future at all, but a dying sub-Universe which the Eternines are trying to escape. Hoping that rescuing Malahyde has changed history, the Doctor tries travelling forward in time to see whether the year 2003 is as it should be -- but instead materialises on a dead beach. By passing through the dimensional rift the TARDIS has entered the Eternium, and it’s now stuck there, unable to escape.
Anji and Gottlieb are succumbing to exposure in a cave, and Anji is dreaming of the Doctor and Fitz, who both tell her she’s going to die. Fortunately, the TARDIS arrives nearby, and the Doctor gets Anji and Gottlieb inside. In order to escape the Eternium, the Doctor connects Anji to the TARDIS so it can use her biodata to locate her home universe -- but it can’t find any trace of her biodata trail anywhere else in time and space. Disturbed, the Doctor tries to do the same with Gottlieb, but as the TARDIS dematerialises Gottlieb begins to convulse. The Doctor stops the others from interfering, insisting that this is their only means of escape. The TARDIS materialises safely, but the process kills Gottlieb, and the scanner indicates that they’re back in the post-Cleansing Totterdown. Not only has the Doctor just killed a man, it seems his actions have failed to restore history to normal.
When the TARDIS materialises, Watchkeeper Fitz Kreiner abandons his post to investigate, unsure why it seems so familiar to him. Anji lets him in and shows him his room, hoping that it will stir memories of his past with them, but Fitz remains confused by his conflicting memories. As he struggles to work out where he belongs, Anji confronts the Doctor about Gottlieb’s death, and Brunel insists that he be given the chance for a proper burial. Though time is pressing, the Doctor reluctantly concedes to their wishes -- but Anji is starting to realise that in the current crisis the Doctor may consider anyone expendable, including herself and Fitz.
The Doctor and Brunel carry Gottlieb’s body out of the TARDIS, and while they try to explain themselves to Foster, Robin slips aboard the TARDIS in search of his friend Fitz. Anji helps the Doctor and Brunel to give the suspicious Watchkeepers the slip, and they return to Ashton Court in the TARDIS. There, the Doctor and Brunel emerge to speak with the elder Malahyde, and the Doctor explains that the Cleansing was a deliberate effect; by accelerating some dimensions of time but not others, the Engine generated a vast amount of energy through temporal friction, which the Eternines intended to channel into their own universe. By interfering when he did, the Doctor prevented far worse than the Cleansing. However, history should have been restored when Malahyde was removed from the Eternium before he was possessed by Watchlar -- and the fact that it hasn’t, and that the Doctor couldn’t locate Anji’s home universe anywhere in time and space, suggests that the universe of the Cleansing is now the dominant timeline after all.
The Doctor seems to have accepted that he can’t change things back to the way they were, and he convinces Aboetta and Malahyde to enter the TARDIS so they won’t be affected when he uses the TARDIS to shut down the Utopian Engine. The younger Malahyde hides in the library when his older self enters the TARDIS, and watches as the Doctor links the TARDIS to the Utopian Engine and brings time within the estate back into phase with time outside. However, as soon as both time zones are back in phase, a blaze of energy emerges from the TARDIS console and envelops Aboetta, and the older Malahyde realises that she’s being possessed by Watchlar. The possessed Aboetta shoots Malahyde dead and leaves the TARDIS, and the younger Malahyde, horrified by what he’s seen, flees into the depths of the TARDIS. Just as he fears he’s going mad, he meets a calm young woman who calls herself Natasha; she’s been paying attention to her surroundings, and assures young Malahyde that since his history diverged from the older man whose death he’s just seen, he need not worry about suffering the same fate.
The Doctor and Brunel pursue the possessed Aboetta into the cellar, where the Doctor tries and fails to reason with Watchlar. When the Doctor pushed the possessed Malahyde into the temporal field in 1843, Watchlar’s spirit merged with the energy generated by the Cleansing to create the temporal field around Ashton Court. By bringing the two time zones back into phase, the Doctor has freed Watchlar, and he’s taken advantage of the foothold he gained in Aboetta’s mind earlier to possess her fully. The Doctor tries to return to the TARDIS, but Watchlar realises what he intends to do and strikes him down with a bolt of energy. Brunel gives his life to push the Doctor out of the way, and the Doctor retreats into the TARDIS, unable to stop Robin from emerging to try to save Aboetta. Inside the TARDIS, the Doctor operates the controls but refuses to tell Anji and Fitz what he’s doing for fear that they’ll try to stop him. Watchlar activates the Utopian Engine and then abandons Aboetta, who finds herself dying in Robin’s arms after all. But then Time goes into reverse...
When the Doctor shuts down the TARDIS, it’s sitting in the cellars of Ashton Court before the Cleansing took place. Since the Utopian Engine was capable of accelerating Time, the Doctor was able to throw Time into reverse; rather than physically travelling back in Time to change the course of history, he’s rewound it, erasing the past 160 years altogether. The young Jared Malahyde returns to the console room, bewildered but accepting what has happened to him, and the Doctor drops him off in the streets of Bristol and sets off for 2003 to see whether reality has been restored to normal. Fitz finds his memories of the TARDIS, and his ability to play the guitar, growing stronger as his biodata rejects the changes imposed upon it by the lost timeline. But he’s still shaken by his experiences and no longer fully trusts the Doctor -- and neither does Anji. Just how far will the Doctor go to fix the damage done to reality... and will even his friends prove to be expendable?