A grey man comes to an English country manor named Shadowfell, where something is wrong with the Universe; but the evil is already stronger than he feared, and as he stands by helplessly, powerless to act, the forces unleashed in the house torture a ten-year-old boy to death and then attack the grey man’s mental matrix. His last act before death is to summon specialists from this frame of reality to deal with the situation. The TARDIS thus materialises in the cellars of Shadowfell, and the furious Doctor emerges to seek the external force which hijacked his ship. As he and his companions search the cellars, the Doctor and Ace realise that a spatial anomaly is changing the architecture about them, and Benny meets a madman, Justin Cranleigh, who attacks her with a knife and then seems to believe that she’s his dead girlfriend Laura. When Justin’s blind lover Sandra Winterdawn arrives, Benny takes the opportunity to escape unnoticed -- only to stumble across something horrendous. As she flees, voices in her mind taunt her with visions of all that she could have been, had things turned out differently in her life. She emerges from the cellar nearly mad with fear, but the grey man finds her and heals her, causing her to forget, for the moment, what she had found.

The Doctor encounters botanist Charles Moore Wedderburn, who believes at first that the Doctor has come from Cambridge to see Professor Jeremy Winterdawn’s experiments. As the Doctor speaks with him, Benny tries to break back into the house through the conservatory, only to be attacked by blood-sucking orchids. As the Doctor tends to her, Wedderburn realises that they are intruders and reports their presence to Winterdawn. Meanwhile, the forces in the cellar finish sculpting their new corporeal forms, and decide to add a new player to the game. A woman whose name is not Jane Page thus arrives at the house, knocks Sandra out and sets off to assassinate Jeremy Winterdawn in the name of the British Republic. The forces, satisfied, plant suggestions in the Doctor’s and Winterdawn’s minds to get them out of the way, and sit back to wait for Armageddon, while the grey god hides nearby, impotent in the face of their insanity.

Ace finds a nursery with a chaotically swirling window, and is attacked by a giant insect which emerges from an empty cabinet. She manages to fight it off, but is then captured by the house’s manservant, Harry Truman -- a man who hides the horrific scars of an accident behind a blank wooden mask. He doesn’t believe her story about the insect and takes her to explain herself to Winterdawn, just as Sandra arrives, claiming that she was attacked by a strange young woman. Since Sandra’s optic nerves were damaged in the car crash which paralysed her father and killed her mother, she is uncertain whether it was Ace who attacked her. Winterdawn orders Truman to bring him the other intruders, and Truman locates the Doctor, who is tending to the recovering Benny while Cranleigh watches. Page attacks them, still seeking Winterdawn, but when she demands to know who they are and Truman starts to tell her, Cranleigh snaps and attacks him, claiming that Truman has stolen his life. The Doctor and Benny overpower the surprised Page and knock her out, while Cranleigh knocks out Truman. Benny removes Truman’s mask, to reveal a sight which proves that there is something unnatural at work in the house.

Suspecting that Winterdawn is the cause of all he has witnessed, the Doctor confronts him, only to find that Winterdawn is unaware of the evil at work in his house. The scientist admits that he has been experimenting with a device capable of manipulating space and time, which his friend Wedderburn found in the Amazon while tracking down mutations amongst the local flora. When the United Nations withdrew funding for his experiments, Winterdawn’s colleague Claire Keightley smuggled the tetrahedron away to him, and he has continued his experiments in the privacy of his own home ever since. Unfortunately, when Sandra’s lover Justin used the tetrahedron to enter the interstices of Time, the forces he encountered there drove him mad. Despite this setback, Winterdawn still intends to understand the secrets of the tetrahedron, and use it to bring about a revolution in society. The Doctor, intrigued, agrees to accompany Winterdawn on an expedition into the interstitial vortex -- despite the fact that it is Truman who will be keeping the tetrahedron “open” to ensure their safe return.

While the Doctor and Winterdawn enter interstitial Time, Benny and Ace return to the cellar to investigate Benny’s uneasy half-memories of an atrocity. Once the coast is clear, two hideously beautiful strangers, Gabriel and Tanith, arrive at the house and remove Sandra’s inhibitions from her mind. She thus confesses to Truman that she loves him, as he seems to embody all that Justin has lost. They start to make love -- and while Truman is distracted, Gabriel and Tanith shut down the tetrahedron. The Doctor and Winterdawn will be trapped outside time and space for all eternity, unable even to die. Gabriel and Tanith reveal that Truman is their creation; when Cranleigh entered the interstices, they found him, took him apart and put him back together in a different way. They built Truman out of the bits left over; he is all that Cranleigh could have been if his life had been slightly different. Truman’s memories of an accident are false, as is his perception of himself; beneath the mask his face is unblemished by scars, or indeed by facial features of any kind. His work is done now, and Gabriel and Tanith unmake him and restore his memories to Cranleigh.

Benny and Ace discover that the cellar is full of savagely mutilated corpses, and try to flee, only to find that Gabriel and Tanith have isolated the house from the rest of the Universe. Gabriel and Tanith are embodiments of universal archetypes, their human bodies shaped from the flesh of those they lured to the house and tortured to death -- because they could. They are psychotic, omnipotent and amoral, and they intend to torture, humiliate and degrade their captives, simply to entertain themselves. Eventually, they release their prisoners into the house and twist its architecture out of all logical sense. Desperate to get the Doctor and Winterdawn back, Ace, Sandra and Benny try to convince Cranleigh to operate the tetrahedron, hoping that the part of him that is Truman will remember how to do so. At first he refuses, still blaming Sandra for preferring Truman over him. Benny, however, pretends to be Laura once again and convinces him to try. He is unable to control the forces unleashed by the tetrahedron, however, and his mind is wiped clean of its identity.

Jane Page revives, captures Ace and Benny, and demands that they take her to Winterdawn. As they search the house, however, Gabriel and Tanith get into their minds to show them the hollow cores at the centre of their beings; they think they know who they are, but it would have taken only the smallest of changes in their past to make them entirely different people. Gabriel and Tanith then show the women to the nursery, where a thousand screaming voices explode out of the window and lash out in rage at Ace and Benny for their lost existences. Benny tries to smash the window, but the power earths itself through her body, killing her. The giant insect which attacked Ace returns; the only survivor of a timeline where its species was the dominant life form on Earth, it is confused and angry to find itself on what appears to be an alien world, and attacks Ace and Page. Page guns it down and comes to accept that the true enemy in the house is not Winterdawn, but Gabriel and Tanith.

Gabriel and Tanith make a slight chemical adjustment to Sandra’s brain, turning her into a raving maniac who murders Wedderburn and feeds him to his own orchids. Page and Ace try to shoot them, but they easily repair the damage caused by the bullets -- and seem to appreciate the pain, which is a new experience to them. They gleefully inform the stunned Page that she is also from a history which never existed; like the insect, Gabriel and Tanith unearthed her potential from beneath the surface of the Universe. Every time traveller erases infinite potential futures from history, simply by being in an age where they do not belong, and Gabriel and Tanith are an expression of the Universe’s pain. As such, they can see anything that can possibly be, and much that cannot -- and they have no morality whatsoever. Gabriel takes Page to the attic, puts out her eyes and tortures her, for no reason at all. Meanwhile, Cranleigh is drawn to the nursery by the voices echoing in his empty mind, and there, the power from the window earths itself into him. He thus becomes the spokesman for the spirits unleashed by Gabriel and Tanith, all who will never have the chance to exist because their potential histories were erased by time travellers. Despite the fact that Gabriel and Tanith embody their pain, however, the spirits refuse to serve them, and Gabriel and Tanith therefore decide to punish them by unknitting Cranleigh’s DNA, causing his body to begin disintegrating slowly.

The Doctor and Winterdawn are trapped in the interstices, knowing that madness will be their only escape… until the grey man arrives. He explains that Winterdawn’s experiments with the tetrahedron have damaged the Universe on numerous levels; on the most basic level of reality, the damage has manifested itself as Gabriel and Tanith. The grey man summoned the Doctor to help defeat the two, but now realises how badly he had underestimated them. He returns the Doctor and Winterdawn to Shadowfell, where they find Sandra traumatised, Truman gone, Jane mutilated, Cranleigh empty, Ace exhausted, and Wedderburn and Benny dead. Winterdawn tries to find and kill Gabriel and Tanith, but on a whim they restore his ability to walk. The Doctor is at a complete loss, unable to cope with Benny’s death and unable to defeat his omnipotent enemies.

Benny’s spirit awakens in a vast and appalling city, Cathedral, where she is greeted by the grey man, its creator. His species was the first to walk the Universe, and to his horror they remade it in their image, setting all who followed them on a meaningless and destructive path of duality -- “good” versus “evil”, “us” versus “them”. Knowing that his people had unleashed madness upon the Universe, the grey man built Cathedral, a metacultural engine intended to spread doubt and uncertainty throughout the Universe and undermine what his people had done. His people cast him out for blasphemy, and ever since then, he has served as Cathedral’s representative in the Universe. The tetrahedron is Cathedral’s extension into reality, and Winterdawn’s meddling has caused it to generate physical forms for the metaphors represented by Gabriel and Tanith. For some reason, Gabriel and Tanith sent Benny’s soul to Cathedral at the moment of her death, but the grey man does not yet understand why.

The grey man offers to give Benny a tour of the city, but before he can begin he is summoned to the Cruakh by the Mandelbrot Set, talking stone heads which straddle the border between order and chaos. They believe that Gabriel and Tanith have become too dangerous, and order the grey man to destroy them. The grey man warns the Set that an apocalyptic confrontation serves no purpose and is against everything that Cathedral stands for, but when they threaten Benny’s life, he has no choice but to do as they demand. He thus returns to reality to confront Gabriel and Tanith, but he is well aware of the hypocrisy inherent in his claiming moral superiority by killing them for acting as agents of chaos. He therefore gives himself up to them and allows himself to be killed. The Set, stunned by this apparent betrayal, attempt to retrench to retain their own power within Cathedral, and order that Benny be killed. At the last moment, however, Gabriel and Tanith arrive and rescue her, and in the confusion the surviving members of the Set turn on each other, each seeking to become the new ruler of Cathedral. As the leaderless myths of Cathedral turn on each other and the city burns, Gabriel and Tanith reveal to Benny that as creations of Cathedral themselves, they had no power here -- but as an outsider, Benny brought chaos in her wake and allowed Cathedral to be destroyed. Once the city has fallen, Gabriel and Tanith will take the seat of power and use Cathedral to remake the Universe in their own hideous, amoral image.

Winterdawn tries to strike a deal with Gabriel and Tanith, offering them the tetrahedron if they agree to restore Sandra’s sight, but instead they tear her apart with their bare hands and take away his ability to walk again. As Cathedral dies, it draws matter out of the real Universe to sustain itself, and Shadowfell and its surviving inhabitants are thus drawn into the city. The Doctor gets to the TARDIS with the tetrahedron, however, thus bringing Cathedral’s physical extension into Cathedral itself and preventing the collapse of the Universe. Jane, driven mad by pain, tries to kill the others, but Cranleigh confronts her and absorbs her into his dissolving body. He then carries the despairing Winterdawn to the Cruakh for the final confrontation with Gabriel and Tanith. The Doctor finds Benny, who was restored to life when her body was drawn into Cathedral and reunited with her soul; they too set off for the Cruakh, while Ace is captured by Gabriel and Tanith and dragged to the Cruakh to witness their triumph.

The seat of power in the Cruakh has been replaced by Winterdawn’s wheelchair, which he had always seen as a trap. Realising that everything that happens in Cathedral is symbolic, he takes his seat and allows himself to die, in order to show Gabriel and Tanith that their actions have consequences. This fails, as they already know, and don’t care. Cranleigh then takes the seat of power, and he and the spirits within him forgive the Doctor for the meddling which erased them from existence. By using Cathedral to ease the Universe’s pain, they rob Gabriel and Tanith of the source of their power -- but Gabriel and Tanith reveal that when Cathedral falls, they will be able to access its essence. But they have forgotten one thing -- the essence of Cathedral is the grey man, and when released it takes on the grey man’s form and identity. Gabriel and Tanith are thus unable to control it, and since Cranleigh’s sacrifice has robbed them of their power, they are vulnerable. Ace kills them both, but finds the act of vengeful murder unsatisfying. She, Benny and the Doctor return to the TARDIS and depart, while the grey man leaves the dead Cathedral behind and sets off to explore the Universe and aid those in need.