As dawn breaks, the Doctor tells I.M. Foreman that he suspects the TARDIS had sensed a terrible change was dawning, and that it had been visiting dimensional rifts in 20th century Earth in order to chart its course and prepare for the worst. But when Sam told the Doctor she wanted to leave, he avoided 20th century Earth until he had no choice -- and when the change came, he was completely unprepared...

Sam comes to realize that the Remote are true anarchists; each member of the society is an individual who acts upon the signals from the media in his or her own manner. The Remote are sterile, and when one of them dies, the dead individual is reconstituted from raw biomass which is given form by the memories of the dead person’s former friends; thus, the next generation copy of the individual is not exactly the same as the one before. This is done to avoid stagnancy, but Sam suspects that the Remote’s ultimate agenda has been changed over the years by the inevitable distortions in the process. Since her only other option is to wander around Anathema until she starves, Sam follows Compassion to the top of the transmitter, where Guest is waiting with the media, a thick black globe of the Cold. Sam is absorbed into the media before she can react, and Guest prepares to analyse the thoughts and signals the Cold picks up from her.

Sarah returns to her home, where Lost Boy explains that the Remote intended to distribute Cold across the world in order to change history and attract the attention of the Time Lords, so they could steal a TARDIS and proceed to the next stage of the plan. Before dealing with COPEX they tried selling samples of their technology to individual countries, and Sarah, remembering the delirious Doctor’s mention of a prison cell and a man named Badar, realizes that he tried to follow their trail and has been imprisoned by a country which had accepted Guest’s deal. With the help of Lost Boy and her establishment contact Jeremy, Sarah is able to identify this country as Saudi Arabia. Kode, meanwhile, realizes that Lost Boy has betrayed them, and he captures Sarah and Lost Boy and forces them to use the stolen detection equipment to lead him to the Doctor’s TARDIS. They locate it in Riyadh, and barely manage to get inside before Arabian security forces can arrest them. Lost Boy overpowers the two terrified Arabian soldiers who have been left inside the TARDIS to guard it, and Sarah locks them in a cathedral-sized cupboard and ponders her options.

Inside the media, Sam experiences the Time Lords’ attack on the colony world Ordifica, reinterpreted for her mind as a BBC sci-fi drama starring Sam and the Doctor versus the bug-eyed monsters who want to use Ordifica’s transmitters to beam themselves through the galaxy. By placing Sam in one contrived scenario after another, the media is attempting to understand her “principles”. Guest and Compassion watch as Sam, captured by an Alien and held prisoner inside an airlock, chooses to expel herself into space rather than let the Aliens force the Doctor to land their ship on the planet. In another scenario, Sam must kill the Doctor when he is trapped in a service tunnel which she must destroy to seal the Aliens out of the colony; in the next, she must destroy the planet and its inhabitants to prevent the Aliens from overrunning the galaxy; in another she must kill the baby who will grow up to betray Ordifica to the Aliens; in another she must kill the helpless animals held captive by the Aliens for DNA experimentation. Guest concludes that her principles are based upon aesthetics; she finds it easier to destroy a whole planet than a single helpless baby simply because of the image it creates in her mind. But Compassion realizes that Guest had another agenda; the media has now taken on the concepts of sacrifice and principles and instilled them in the Remote. Before, the Remote would have given up their mission due to any random transmission; now, however, they will risk anything to do so. But Compassion finds that she will no longer serve Guest if it means risking her own life, and she realizes that each member of of the Remote will end up with an individual set of principles, and defend them to the death -- and the result could be civil war.

Kode begins to pick up signals from the TARDIS itself, and rescuing the Doctor becomes his overriding priority. They are unable to find the Doctor due to the Time Lord defenses in his biodata, but they are able to locate the surveillance device which Sarah gave the Doctor while they were suspended in the TARDIS store room. They materialize in the prison cell and use stun weapons to incapacitate the guards beating the Doctor, but the Doctor tells his rescuers that he’s already gone mad. As he slowly recovers within the TARDIS, he assures the worried Sarah that this was only a figure of speech; however, to keep his promise to Badar, he makes one stop in Shoreditch before setting off in search of the Cold. Kode, however, picks up the new transmissions from Anathema, acquires the concept of sacrifice, and threatens to kill himself unless the Doctor takes him back to Anathema immediately. The Doctor takes Sarah back home, promising to return once everything’s been sorted out, and takes Kode to Anathema -- where he finally recognizes Kode’s body language and realizes who he is, or rather, who he was...

Fitz and the other survivors from Ordifica are transported to the 18th century by Mother Mathara and the agents of Faction Paradox, to build a new world for themselves somewhere the Time Lords would never dare to look for them. They will be left to their own devices and will reach the Earth within two hundred years, and Mathara will return only once to see how they are getting on. The leader of the media, Nathaniel Guest, suspects that the Faction is turning them into remote drones for a planned war with the Time Lords. Fitz, meanwhile, finds that he has a natural affinity for the musical mathematics used in the colonists’ computer languages, and is nicknamed “code-boy” by Laura Tobin, a mocking young woman who tells him that compassion is her middle name. The members of the new culture have been programmed with time-travel biodata, but this has rendered them sterile, and they will only be able to procreate by cloning tissue from biomass and recreating their past selves from the memories of those who survive them. Four years have passed for Fitz since he was kidnapped from 20th-century Earth, and he now accepts that the Doctor is never coming to rescue him -- and fears that he will give himself up to Faction Paradox in desperation when they return. His only alternative is to kill himself now, while the people around him still remember him as Fitz, and hope that the nth-generation copy which is eventually reunited with the Doctor is thus as close to the original Fitz as possible. But is he really capable of going through with it...?

Llewis arrives at the Remote’s warehouse to collect the Cold, only to find them packing up, since they no longer need to use the Cold to destabilise Earth’s history. Llewis refuses to have gone through all of this for nothing, and orders his employees to begin loading the Cold onto their vans. The Remote agents therefore call through a bomber for a kamikaze strike, and Llewis flees through a transportation gateway to Anathema moments before the bomber hits the warehouse. There, he finds that the Cold is seeping up through cracks in the world upon which Anathema was constructed. Meanwhile, Compassion releases Sam from the media and takes her to a fighter; civil war has broken out just as she feared, and she wants to escape from Anathema. When the fighter launches, Sam finally sees that Anathema was constructed on the surface of a gigantic Time Lord warship, constructed during the future war against an unknown, time-active Enemy; it is the one place the Time Lords would never dare to look for fear of drawing attention to it. Sam is shocked when Compassion explains that the warship has been primed and aimed at Earth as the ultimate deterrent; by destroying such a vitally important planet -- which as it happens is the home of the Enemy -- the Time Lords would collapse the causal nexus of history, wiping out both themselves and the Enemy together.

The Doctor lets Guest into the TARDIS, which Guest uses to collect Sam and Compassion in order to force the Doctor to obey him by threatening Sam. He now reveals that the weapon they have been selling is only the skin of the Cold; the Cold itself is one of the loa, the Spirits worshipped by Faction Paradox, which exist on the other side of the dimensional rifts opened by the Time Lords’ past experiments. The Cold can only be reached by a TARDIS, which is why he has been trying to capture one. The Doctor is forced to take him to the Cold, and Guest is absorbed into it -- but when the Doctor learns that the skin of the Cold has been seeping out from beneath the surface of a Time Lord warship, he realizes the truth. The Cold is not a spirit, but a validium-based weapon which exists on the border between the Universes; the screaming faces on its skin are images from the other side of the rifts. The warship, when activated, will re-open one of those rifts, causing the entire target planet to be sucked through into the other Universe to be torn apart by the evils that lurk there. The Doctor tries to communicate this to Guest through the media, but he doesn’t understand that the Remote communicate through images, not words, and it’s left up to Sam to do so. She manages to reach Guest with the truth just as he is about to release the Cold, and, finally realizing what he was about to do, Guest instead orders the warship to dematerialize and travel to a place of safety.

Guest’s decision puts an end to the Remote’s mission, and the Doctor pilots the warship to where it will never be found so the Remote can get on with rebuilding their society. Kode and Compassion have been exposed to too much new information and no longer fit in on Anathema, and the Doctor therefore allows them to accompany him in the TARDIS. First, he takes Sam back to 1996 Earth, where Sarah agrees to let Sam stay with her until her younger self leaves with the Doctor; in the meantime, Sam will help Sarah to complete her story on the “internal security” markets and expose them for the cult-like cliques that they are. Perhaps people will finally start demanding answers. The Doctor doesn’t tell Sam that he’s already gone back to the attic in Shoreditch, where he told her drugged-out younger self about the future; the Earth will fall into chaos and anarchy, only for the same old political patterns to recur. Young Sam concludes that politics are all based upon the meaningless biology of the top ape making all the rules; she must start a cultural revolution, not a political one. The Doctor leaves, satisfied that he’s fulfilled his promise to Badar and given Sam a new life beyond the TARDIS. He then uses the TARDIS data banks to give Kode back his memories of being Fitz, thus restoring him to his old self. Unfortunately, in all the confusion, the Doctor has forgotten about the two Arabian soldiers who are now wandering lost in the depths of the TARDIS.

That would appear to be all, but the Doctor is still certain that he’s missing something important; that something changed for the worse while he was in the prison cell. He doesn’t know what it is, but he feels that it’s connected to his experience on Dust. I.M. Foreman resumes her part of the story...

The Remote have occupied the village, and Magdalena is waiting, knowing that she only has one shot and unwilling to waste it. The Third Doctor and Sarah, meanwhile, learn that I.M. Foreman is a priest from the early days of Gallifrey’s history, driven into the wilderness by Rassilon’s dissolution of the monasteries. He and his fellow freaks have dedicated themselves to showing the people of the Universe what they can achieve if they set themselves free of their preconceptions, by pushing the limits of the biologically possible. The caravan is a complex space-time event like a TARDIS uncontained within a structure, and it weaves a new shape for itself on each world to which it travels. The Doctor realizes that the caravan thus creates pockets of temporal instability to which other travellers are drawn -- just as he and the Remote have been drawn to it on Dust, and just as he was drawn to it when it took the form of an urban junkyard in London, 1963. All this time the Doctor has considered himself to be a pioneer, but I.M. Foreman was one step ahead of him. The Doctor, upset, realizes that he was never supposed to know this; ever since his timestream crossed that of his future incarnation, he’s been feeling out of his depth, as though he’s wandered into an adventure he isn’t ready to cope with yet. Meanwhile, a Faction Paradox warship arrives in orbit, and its crew releases a biodata capsule and waits to see what will happen next...

The leader of the Remote, a former Father of Faction Paradox, threatens to start killing the townspeople unless I.M. Foreman surrenders his caravan to them. Once he realizes who the Doctor is, the Father also plans to kill him -- for the Father is the original Fitz Kreiner. Ever since he chose to join Faction Paradox rather than kill himself in Anathema -- although he left a copy of his biodata behind so the Remote would not lose his talents -- the 2000-year-old Father Kreiner has hated the Doctor for abandoning him. The Doctor, Sarah, and twelve of the thirteen members of I.M. Foreman’s travelling show emerge from their caravans to confront the Father, and I.M. Foreman reveals that the other members of the show are his own future incarnations. By absorbing all manner of animal and vegetable material into his body and incorporating the DNA fragments into his regenerations, I.M. Foreman has pushed his body to the limits of biology, becoming more and more inhuman with each incarnation. He found all twelve of his future incarnations lying in the wilderness of outer Gallifrey after some traumatic experience which had erased their memories; with no idea how they came to be together, they decided to form their travelling show. I.M. Foreman now reveals that his final, thirteenth incarnation, is simply a mass of undifferentiated life energy which seeks to absorb all around it in order to achieve the ultimate goal of becoming everything at once -- and now that the Remote have made their ultimatum, I.M. Foreman has had no choice but to set it free.

Number Thirteen eats the Remote ship and all aboard, and the Doctor and Sarah flee back to the TARDIS as it heads for the town centre to confront I.M. Foreman and the Father. The Doctor uses the TARDIS to manipulated the structure of I.M. Foreman’s caravan, and seals his first twelve incarnations within a copy of the TARDIS police box shell. At I.M. Foreman’s request, he sends the caravan back to ancient Gallifrey, and since it has not created a new shape for itself on that world, it explodes upon being disconnected from the Doctor’s TARDIS. He and his eleven future incarnations are mortally injured, so traumatically that each of them regenerates into the next in line. When I.M. Foreman’s first incarnation arrives, having been cast out of the monasteries, he finds his second through thirteenth incarnations lying in the wilderness with no memory of how they got there. Back on Dust, the Doctor emerges from the TARDIS to confront Thirteen, and points out that since it has eaten the Remote’s biosphere manipulation system along with the rest of the ship, it now has the power to transfer itself into Dust’s biosphere. It does so, thus becoming the planet’s entire ecosystem. From this day forth, Dust will no longer be a dead world, but a fresh and vibrant planet teeming with life -- Foreman’s World.

Before the satisfied Doctor can return to the TARDIS and leave, Magdalena confronts him, blaming him and his fellow travellers for bringing danger to her village. Before he can react, she shoots him fatally in the chest, and as the weeping Sarah drags him back to the TARDIS, he begins to regenerate, knowing only that something has gone terribly wrong. The Faction Paradox cultists watching from orbit -- including Mother Mathara and Brother Llewis, a new recruit from 20th-century Earth -- are dissatisfied, but retreat aware that they’ve won a consolation prize. The Faction had encountered I.M. Foreman in the past and had guessed what his ultimate destiny was to be, and they had released their biodata virus on Dust in the hopes that it would turn Foreman’s World into a living planet of Paradox. Instead, the virus has infected the Doctor due to his unscheduled regeneration. His Time Lord defenses will fight off the infection for some time, and his next few incarnations will be much the same as they always were; however, the change has begun, and by his seventh or eighth incarnation, the virus will tip the scales. First he will lose his shadow, and then a false one will return -- and soon he will become an agent of Paradox...