The Second Doctor believes that he has found a way to bypass the anti-theft protocols which have so far prevented him from steering the TARDIS properly, but in order to do so, he has had to disconnect certain fail-safe systems. When he attempts to materialise in 20th-century London, the TARDIS goes into spasm, and apparently materialises just outside the city of Lychburg in the American Midwest. Shortly after the Doctor and his companions emerge, they witness a terrible car crash, and although it is too late to save the young man in the driver's seat, the Doctor finds and decides to help an unconscious young woman who had been thrown clear of the car before it burst into flames. When he tries to fetch medical equipment from the TARDIS, however, he finds that the dimensions of his ship have shifted, making it impossible to enter. He, Jamie and Victoria fashion a makeshift trellis and try to drag the young woman into town for help, but they are confronted by police officers and placed under arrest. The Doctor is questioned by police chief Clancy Tilson, and learns that there have been a number of gruesome murders in town recently -- and although the modus operandi is the same in each case, some of the murders have occurred on opposite sides of town within minutes of each other.

Katharine Delbane is an agent of the British government's Provisional Department, a network of secret agents which reports directly to the Prime Minister. Her current mission is to infiltrate UNIT, expose its secrets and bring it directly under the aegis of the British government. While searching vainly for some evidence of what it is that UNIT actually does, Delbane locates the disused laboratory of one Doctor John Smith, UNIT's former unpaid scientific advisor, and while she is searching the laboratory, UNIT is raided by what appear to be men in black combat suits, armed with anaesthetic dart guns and spray. RSM Benton manages to warn Delbane before succumbing to the effects of the gas, and she tries to call for help on an emergency field telephone she found in Doctor Smith's laboratory. The telephone doesn't seem to work, however, and before she can flee she is confronted by one of the attackers -- who does not appear to be entirely human. As he sprays her with anaesthetic gas, she goes down chanting alien words which she has never heard before in her life. When she awakens, she learns that Brigadier Lethbridge-Stewart has been kidnapped, and Special Branch and the Provisional Department have taken charge. Her department head, Crowley, tells her that due to this fiasco, British UNIT will be disbanded and its responsibilities will be taken over by the Provisional Department, and Delbane realises that she's been used as a pawn by Crowley to increase his own department's political power.

Once again, the Fourth Doctor has forgotten K9 while departing from his latest adventure, and has been forced to turn time and space upside-down looking for him. He and Romana eventually track down the dormant K9 in the Big Huge and Educational Collection of Old Galactic Stuff, a planetary museum owned by a race of loathesome shape-shifters, but as the Doctor's cunning plan to retrieve K9 consists of smashing a hole in the display case, grabbing him and running, they barely escape with their lives. Before the Doctor can set about repairing K9, the TARDIS is halted by a Time Lord Councillor named Wblk, who informs them that a prototype time machine from early Gallifreyan history has collided with a controlled singularity on a populated planet, creating a dimensional rift which threatens to consume the Universe. Before Wblk can go into more detail, however, the Doctor receives a distress call from an old friend, and sets off to answer it, telling the furious Wblk that the Universe can look after itself for a change. The TARDIS thus materialises back in the Doctor's old laboratory at UNIT, right before the eyes of the shocked Provisional agents Slater and McCrae.

The Second Doctor, knowing that something evil is lurking in the city, checks himself and his companions into a single room in a fantasy-themed motel, seemingly unaware of Victoria's embarrassment. The next morning, he rents a car with money he made selling his blood, and takes Jamie and Victoria to the hospital to check on the young woman they rescued, who appears to have suffered amnesia due to her concussion. The Doctor and his companions, however, note that she and her doctors are not behaving realistically -- it is as if they are actors playing parts, but are unaware of the fact themselves. The Doctor ventures out to the town limits, where he finds that the town is dimensionally self-enclosed; any journey out of town leads one back in without having changed direction. In Lychburg itself, icemen on horse-drawn carts deliver their wares to mini-marts selling microwaved burritos, while '50s rockers hang out on the streets along with people using mobile phones. It is as if someone or something has simply filled the town with symbols of the American Midwest without thought as to the temporal or cultural context -- and this something is controlling the city's inhabitants like actors in a play, driving them to murder each other at whim.

As soon as the Fourth Doctor's identity is confirmed by Benton, he returns to his laboratory and whips up a mish-mash of electronic equipment; this, he claims, will give a holistic overview of London's traffic, and enable him to calculate a chaos equation and locate the kidnappers' most probable escape route. Crowley, apparently believing that he's talking gibberish, assigns the useless Slater and McCrae to escort Romana to the place where the Doctor believes the Brigadier is being held. Delbane, meanwhile, is coming to realise that the happy family atmosphere she'd found at UNIT was not due to a lack of discipline, but was because the people there were fighting for a genuinely good and noble cause; and by helping Crowley to take over UNIT, she has spoiled all of that. She takes out her frustrations on the Doctor, who realises from a chance remark of hers that his equations have been rigged; some external force has imposed a false pattern on the seemingly random London traffic, and the Doctor has sent Romana into a trap. Before he can do anything about it, Crowley drops his facade, pulls out a gun and reveals that this has all been an elaborate trap to lure the Doctor to him. When Delbane, furious, tries to arrest Crowley, his eyes blaze with light, and her will is subsumed to his. The Doctor has no choice but to allow Crowley and his new hostage into the TARDIS.

Romana, Slater and McCrae are ambushed by the black-clad, semi-human soldiers, and taken to Tollsham USAF base. The base is surrounded by protestors carrying Wiccan symbols of protection, which makes it an ideal location for the mysterious Section Eight. Major Joel Haasterman is here, awaiting the arrival of his point man in the UK, and keeping in touch with Dr Sohn back in America, where the Golgotha Project is in the final stages of collapse -- a disaster which could destroy the entire fabric of reality. Romana is flung into a cell with the Brigadier, who is delighted when she reveals that the Doctor is nearby; however, before they can compare notes, Romana is taken away to be interrogated by the base's misogynistic commander, who wants to know just what Section Eight is up to in his base. However, he has never encountered a Time Lady with preternatural reflexes and a chemical resistance to sodium pentothal before, and eventually he is forced to give up and throw her back in a cell by herself. There, she is contacted once again by Wblk, who reveals that the Time Lords allowed the Doctor to escape, because he was going to the right place anyway...

When the Second Doctor's car runs out of gas near the Shady Pines Shopping Mall, he decides to explore it, theorising that the entity in control of Lychburg may have made its home where large numbers of people naturally congregate. They are soon split up by the random motion of crowds in the large structure, and the entity, who has been trying and failing to control the new arrivals' minds, seizes the opportunity to send its possessed townsfolk after them. Victoria is attacked while trying to buy clothes at the GAP, and Jamie is captured by barflies who, in the middle of an ordinary day, suddenly start discussing how annoying it is that they've had to murder all their friends and loved ones recently. The Doctor, browsing in a sci-fi and comic book store, finds a '50s pulp SF periodical in which the words of the stories are changing as he watches, and realises that this entire mini-Universe is on the point of catastrophic collapse. When he tries to reach out to the entity and warn it of the danger, however, it pinpoints his location and captures him as well.

The Fourth Doctor pilots Crowley and the dazed Delbane, who is starting to feel as though someone else is watching events unfold through her eyes, to Tollsham base in the TARDIS. There, Crowley is revealed to be Aleister Crowley himself, who was recruited by the Americans in World War Two in much the same way as former Nazi rocket scientists, and for much the same reasons. It appears that the upper echelons of the Nazi government had had some small success in using magic to gain personal power, and as the Cold War descended, the Americans decided to investigate the military possibilities of magic. The population of a small Midwestern town, Lychburg, was brainwashed to believe anything they were told, instantly and without question; then, after faking his own death, Crowley supplied the Golgotha Project with a magical artefact capable of transforming belief into reality. To test the military applications of the Project, the army convinced the population of Lychburg that the gates of Hell were opening, and thus created a dimensional rift -- which was then destabilised when something collided with it, causing it to expand. To prevent the rift from consuming the world, the Americans launched a nuclear strike which knocked it out of dimensional alignment, transforming it into a stable singularity. But now, decades later, something has destabilised it again, and they desperately need the Doctor's expert help to contain it before it destroys the world.

The Second Doctor, Jamie and Victoria are taken to the Lychburg Drive-In, where the entire population of the city, drawn by a force they neither understand nor notice, clamber onto one another's shoulders and are united by an alien energy into a giant humanoid figure, an Avatar of the entity controlling them all. Doctor Dibley attempts to implant a transceiver in the Doctor's neck to bring him under the entity's control, but the Doctor slips away at the last moment -- and accidentally causes Dibley to fall onto his own scalpel, killing him. For the first time ever, someone under the entity's control has died by accident, and the shock drives it momentarily senseless, giving the Doctor, Jamie and Victoria time to escape. Realising that the entity is hidden behind the drive-in screen, the Doctor investigates to find the wreckage of a prototype time machine from his home world -- and a test animal which had been placed aboard the machine, the last Gallifreyan woprat in existence. The woprat leaps at the screaming Victoria, and before the Doctor can stop him, Jamie kills it with his dirk. Not only has he just killed the last woprat in the Universe, he's killed the entity which was controlling this Universe, and within minutes it will collapse entirely and take everyone inside with it.

The Fourth Doctor refuses to help Crowley and Haasterman unless it's on his terms, but they threaten to shoot their hostages one by one unless he uses the TARDIS to bring the singularity under their control. Romana, however, offers to do so herself, claiming not to be concerned should the human race wipe itself out. Crowley and Haasterman thus allow her to operate the TARDIS controls, but instead of using them to restabilise the singularity she materialises within it. The shock of their arrival distracts the others just long enough for the Doctor and Romana to escape into the corridors with the other hostages. Crowley, furious, drops all vestige of his human form and speaks a Word of Power which transforms Haasterman's soldiers into demonic minions. The minions tear Haasterman apart and pursue the prisoners into the depths of the TARDIS, where the Doctor, Romana and Delbane have been separated from the Brigadier, Slater and McCrae. As they flee, Romana informs the Doctor that the Golgotha Project is the dimensional rift the Time Lords wanted them to fix -- and that its current unstable condition was caused by the Doctor's own TARDIS, at another point in its own timestream, materialising within it.

The Doctor and Romana thus make their way to the ancillary generator room at the heart of the TARDIS, which has, thanks to the nature of the singularity, now become linked to the same point within the Second Doctor's TARDIS. Before they can pass through, however, "Crowley" arrives and identifies himself as a Jarakabeth, one of a race of energy beings or demons; he replaced the real Crowley at the moment of his death, and has used the Golgotha Project to unleash chaos upon the Universe and remake it in his own image. He draws the life force out of his minions and attempts to kill the Doctor and Romana, but Delbane suddenly drops her own human guise, revealing that she had been sent some time ago to keep an eye on him. While she holds Crowley off, the Doctor and Romana enter the nexus point, and after a subjective 15-year journey through the nether dimensions and a number of extraordinary but irrelevant adventures, they appear in the Second Doctor's control room. There, the Fourth Doctor puts the interior of the TARDIS back into phase with the outside, and he and Romana then hide. His earlier self, finally able to re-enter the TARDIS, takes a few readings and then rushes back out to deal with the collapsing mini-Universe, and the Fourth Doctor, finally understanding how he was able to get back into the TARDIS during that particular adventure, smacks himself for fiddling around with his own TARDIS without permission. He then returns to the nexus point with Romana, who is rather disgruntled to realise that they've gone through everything they've just gone through simply in order to open a door.

The Brigadier, Slater and McCrae finally reach the ancillary generator room, where they see Crowley and Delbane floating in mid-air as the entities within them do battle on levels which humans cannot perceive. Unfortunately for Crowley, he's forgotten about the most basic level of all, and is thus utterly unprepared when the Brigadier reaches out and tries to drag him out of the air. This momentary distraction enables Delbane to get past Crowley's defenses and destroy him utterly. When the Fourth Doctor and Romana return, the creature inside Delbane apologises for the criminal Crowley's behaviour, and informs them that it will now retreat back into the depths of Delbane's mind, allowing her to live out the rest of her human life in peace without realising her true nature.

The Second Doctor does something terribly clever, thus saving the lives of everybody in Lychburg, which is transported back to the real Universe when the singularity collapses. He, Jamie and Victoria then set off on their travels once again before awkward questions can be asked, but the Doctor is still upset with Jamie for killing the last Gallifreyan woprat in existence -- and with himself, for inadvertently causing Dibley's death. Back in England, the recovering Delbane decides to join UNIT, while the Fourth Doctor and Romana set off to resume their quest for the Key to Time. Unless something else turns up... which, where the Doctor's concerned, is pretty much inevitable.