Nobody at St Benedict’s School in Perivale is quite sure how to react when young Chad Boyle hits his playmate Dorothy in the head with a brick, killing her. As a junior, Chad is remanded into the custody of his mother until a punishment can be decided upon, but late one night a police box materialises in his bedroom and a sleepwalking man takes Chad away to kill Dorothy again. Some years later, in 1992, the Reverend Ernest Trelaw of Cheldon Bonniface speaks with Saul, the disembodied spirit which inhabits his church; both can sense a change in the air, and they feel that perhaps their old friend the Doctor is on his way. There are two newcomers in Trelaw’s congregation; mathematician Peter Hutchings and his wife Emily, who does not realise that she is mildly psychic. Emily is still trying to deal with the recent revelation that she is unable to bear children, and she too is disoriented by the sense that something wondrous is soon to come. Halfway through the service she realises that she can perceive Saul’s presence -- and when the Doctor walks into the church, hands her a baby and walks out again, she faints dead away.

Ace, disturbed by restless dreams, takes no comfort in knowing that the Doctor too is suffering from sleepless nights; she fears that he continues to travel while she sleeps, setting complex plans in motion without her knowledge. The TARDIS materialises in Cheldon Bonniface during the Victorian era, and while the Doctor plays chess with his old friend George the innkeeper, Ace retires to her room at the inn -- only to be attacked by an astronaut the size of a child. She manages to struggle free and flees, but emerges from the other side of the woods to find herself on the surface of the Moon. Her momentum carries her beyond the atmospheric bubble around the village, and she passes out from lack of oxygen. The young astronaut, her childhood nemesis Chad Boyle, carries Ace to the village church, and uses a device given to him by his Angel to send her mind to a place which the Angel cannot reach herself, but where a familiar personality will be granted access…

The Doctor, realising that George is an impostor, escapes from his clutches and flees to the church -- but when he fails to find what he’s looking for there, he is forced to return to the pub to find out what’s really going on. There, “George” disposes of his disguise to reveal that he is in fact Lieutenant Hemmings of the Britischer Freikorps, removed from his own timeline by a being he believes to be one of the ancient Norse Gods, and sent to lure the Doctor into its trap. The Doctor evades him once again and flees to the TARDIS, and his real enemy, realising that Hemmings has been outwitted, disposes of the Cheldon Bonniface illusion, maintaining only a small atmospheric bubble to keep Ace’s body alive. It possesses Chad Boyle fully, reshaping his body into the form of a small dragon and sending his mind after Ace to torment her further. The dragon kills Hemmings for his failure, striking his head from his body with one powerful blow, and sends Hemmings’ mind after Ace as well. It then waits for its preparations to bear fruit, and for the Doctor to arrive…

Ace awakens on what appears to be a desolate pier in Cromer, where a friendly receptionist tells her that she is dead; the Doctor gambled her life against his enemy’s plans, and lost. She is transported elsewhere to face judgement and finds herself in a vast library, where the elderly Librarian shoos away the menacing clowns emerging from the shadows and ushers Ace into a reading room. There, she finds a pack of Tarot cards with images from the Doctor’s life on them, and shining silver tentacles drag her into a globe representing the Universe and deposit her on an endless black wall. She blows a hole in the wall with her nitro-nine and passes through into a room with thirteen cubicles; seven are empty and the remaining six contain inchoate humanoid forms. A voice claiming to be her rational side tells her that she is having a nightmare, and that if she closes her eyes and concentrates upon Cheldon Bonniface, she will wake. She does so, but a terrible power then floods through her, knocking her senseless. In the TARDIS, the Doctor goes into spasm and sticks his hands into the exposed telepathic circuits -- and in Cheldon Bonniface, Saul senses some terrible force locking onto him, and shouts out a warning. The congregation flees in panic as Trelaw tries to help the confused Peter and Emily -- but the three of them are still in the church when it becomes the epicentre of an explosion which levels everything within two miles.

The Doctor recovers and pilots the TARDIS to Ace’s body to confront the dragon. He knows it for what it is -- the Timewyrm, whose existence was foretold by ancient Time Lord prophets, whose feeding will break the chains of causality and bring the Universe to a premature end. He offers it mercy, but it rejects his offer, certain that it has the upper hand. St Christopher’s Church then materialises on the Moon, bringing with it the surprised Trelaw and the Hutchings. Saul discovers that the force of their departure has destroyed the village and all its inhabitants, but the Doctor urges the shaken new arrivals to remain calm; they have been brought here by an ancient evil, and must remain clear-headed for the battle to come. The Doctor removes an amulet from a crevice which even Saul did not know existed, and gives it to Emily, telling her that she will know when to use it. He then confronts the Timewyrm, who raises Death from the lunar dust and takes the Doctor’s life. The Timewyrm then animates his body, marches it into the church and lays it down next to Ace’s, and vacates the dragon’s body to follow her enemy into death. Trelaw, Saul, and the Hutchings -- and the strangely unresponsive baby -- remain in the church to await whatever will happen next.

Ace awakens in Hell’s waiting room, her memories fragmented and confused, unable to shake the persistent conviction that Chad Boyle killed her when she was eight years old. The jeering Chad drags her back to their school, where she becomes a child once again, helpless to change the injustice in the world around her. The Doctor arrives to rescue her, but Ace is infuriated to see him in Hell; not only did he get her killed, but he’s sacrificed his own life out of guilt about it. She storms out of the school to find herself in a rose garden, her maturity restored. There, she meets the Librarian, who is trying to control an infestation threatening to destroy the garden. Chad pursues Ace and conjures weapons out of thin air, but Ace overpowers him. The Doctor intervenes, trying to stop Ace from killing Chad, but this drives another wedge between them; the Doctor has destroyed whole planets, and yet he doesn’t trust Ace to know right from wrong? Eventually she calms down enough for him to explain where they really are -- not Hell, but the computer system or living mind which the Timewyrm is currently using as a host. Only if they reach the Pit in the centre will they be able to escape.

Still trying to drive a wedge between the Doctor and Ace, the Timewyrm confronts them with the spirits of those whom the Doctor has failed to save, including his former companions Katarina, Sara Kingdom and Adric. Ace leads the Doctor past them into the next zone of the datascape, but to the Doctor’s horror it has been replaced with an idealised Nazi city ruled by Hemmings. The lieutenant is torturing the zone’s former inhabitant, a white-haired man whom the Doctor seems to know. Hemmings now prepares to torture the Doctor, but to Ace’s shock the Doctor begs Hemmings to spare him and take Ace instead. Amused, he does so, and the Doctor is thus given the chance to confer with the prisoner. After helping the Doctor in Mesopotamia, the Prisoner was troubled by dark thoughts, and while meditating upon them he came to realise a terrible truth. Once, he visited an alternate timeline in which England was ruled by a fascist dictatorship -- and he now knows that the leader depicted on their posters wore one of the faces which the Time Lords had offered him at his trial. Overcome by his own demons, he offered little resistance when Hemmings arrived to make the place his own. The Doctor, understanding, joins his mind to the Prisoner’s, to get a message to the outside world while they still can.

Peter, still trying to comprehend what is happening, points out that although Saul has detected no signs of life within the Doctor, his eyelids are still twitching, as though he is dreaming. Saul finds a tune running through his head, a complex melody like an epic poem or mathematics set to music -- and as he hums it, nobody notices that the gemstone is pulsing in time to the beat, or that even the baby seems to be responding to it. Peter realises that the beat represents a chaos equation, and is able to calculate a response which Saul hums. He receives another verse in response, which seems to be instructing them to find a severed human head outside the church. Saul locates and telekinetically transports the head of Lieutenant Hemmings into the church, and despite Trelaw’s objections, Saul and Emily try to communicate with the life inside the dormant brain. This draws Hemmings out of the datascape and back into his own severed head, where he dies -- but his removal throws the datascape into chaos, and as the Timewyrm scrambles to regain control, the Doctor and the Prisoner escape and make for the border. There, a Ferryman wearing a floppy hat and long multi-coloured scarf is waiting to convey the Doctor to the Pit.

Ace, lost in the chaos, awakens to find herself in a picture-perfect world with a loving family and cool friends. All she does all day is talk about boys, fashions and music -- and to keep this world, all she has to do is ignore the people begging for money on the street corner, and the gang of white youths assaulting a Pakistani girl outside the disco. But she can’t stand by and let the injustice continue without challenging it; she is not Dorothy, she is Ace. She drives off the white youths, recognising the girl as her old friend Manisha, and as she beats her anger out on the wall of the disco, the blood from her hand reveals a door. She enters, seeking the Doctor, and as the world collapses behind her, torn down by her anger, the Third Doctor -- a prisoner no longer -- begins to rebuild it in his own image once again.

In the wasteland around the Pit, the Doctor is confronted by Chad Boyle, who stabs him in the side with a sword. Ace arrives and drives Chad off, but the Doctor has already suffered a fatal wound. As she carries him to the Pit, he tells her that the Timewyrm still does not understand its true nature; as a living function of the Universe, its form is shaped by fractal equations, which the Doctor has used without its knowledge. In the church, as the Doctor’s physical body begins to die, the amulet expands into a portal to the Time Vortex, and Saul realises that the poem he is intuiting can be used to calculate a safe path through. If Peter helps him with the equation, then Saul can guide Emily through the Vortex to rescue the Doctor. Emily accepts the responsibility.

Ace takes the Doctor to a bridge over the Pit, where the Timewyrm is waiting for him to die. It reveals to Ace at last that they are inside the Doctor’s own mind; the Timewyrm planted a seed of itself within him when he summoned his third incarnation to the surface in Mesopotamia. By sending Ace, a familiar presence, into the Doctor’s mind, it was able to access parts of his psyche which he had blocked from it, and thus channelled the burst of psychic energy which brought Saul to the Moon. When the Doctor followed Ace into his own mind to rescue her, he became vulnerable to the Timewyrm’s attacks, and when he dies, the Timewyrm will channel the psychic energy of his death through Saul and crash the Moon into the Earth. Billions of timelines will be destroyed, and the Timewyrm will gorge itself upon the energy and grow more powerful still. In the Doctor’s body, it will then travel back in Time to have Chad kill Ace as a child -- and the fact that she can remember this happening seems to prove that the Timewyrm’s plans will succeed.

But just as the Timewyrm appears to have triumphed, a shining staircase descends from the sky, bringing Emily with it, and while the Timewyrm is distracted the Doctor uses the last of his strength to fling it into the Pit. He bathes himself in the water cascading down the staircase, a representation of the psychic power flooding from Saul, and the damage to his virtual body is instantly healed. This has all been a complex game of the Doctor’s, and they have one chance to win. But the Doctor still has not dealt with his own guilt and fear of failure, and as he, Ace and Emily flee up the staircase, the Doctor’s personal dead rise from the Pit and pursue them. Ace falls into their hands, and, realising that the Doctor will be dragged back if he tries to save her, she gives herself up to them, releasing the Doctor into the Vortex tunnel. But once his mind and body are reunited in the church, he faces an agonising choice, for he has gambled and lost. Knowing that the Timewyrm had invaded his mind, he had concentrated on building up his mental defenses until he was ready to set a trap for it. Using Ace as bait, he tricked the Timewyrm into committing all of its resources to a battle within his mind. Now, thanks to Saul and Emily, he has escaped, and the Timewyrm is trapped in his mind with no way out. But so is Ace -- and if the Doctor crushes the Timewyrm out of existence as he had planned, then Ace will die as well. Yet what other choice does he have?

Ace is released by the dead, who tell her that to save herself and them, she must descend into the Pit of the Doctor’s subconscious. He has buried his conscience out of what he believes to be necessity, but it is his failure to acknowledge and deal with his guilt which keeps the dead in torment within his mind. Ace descends into the Pit, where she finds the Fifth Doctor tied to a tree as punishment for refusing to join the others in their fight. The Timewyrm is there as well, with Chad Boyle, waiting for the Doctor to kill them -- knowing that his guilt over Ace’s death will haunt him, and cause his memories to resurrect the Timewyrm once again. Chad tries to stop Ace from freeing the Fifth Doctor, but when she prepares to fight she finds her memories fading away again and realises that this is just what the Timewyrm wants. Instead, she forgives Chad, and looks past his bullying exterior to what he really is -- a frightened child who has had enough and just wants to go home. Ace releases the Fifth Doctor, restoring the conscience which the Doctor had tried to bury; but the enraged Timewyrm summons archetypal horrors from the Doctor’s collective unconscious and sets them upon Ace and Chad…

The Doctor finds that he cannot bring himself to kill Ace; instead, he will risk all that there is to find another way. Telling the others to wait in the church, he pilots the TARDIS into the interface between imagination and reality, to an arena within his own mind where the Timewyrm is waiting for him. To its shock, however, it finds that it cannot harm him unless he wishes it; he had only allowed it to do so earlier to convince it that it was winning. He comes now not to kill it, but to offer it peace. Terrified by what he promises, the Timewyrm destroys Chad’s body, bursting out of it to attack the Doctor -- but he stands up to the attack, reaches into the archetype that the Timewyrm has become, and finds the human life at its core… Qataka, who is tired and just wants to go home. The Doctor takes her essence into himself, and as the Timewyrm settles into dormancy within the structure of the Universe, he uses its power to change history on Earth and ensure that Cheldon Bonniface is not destroyed. Nobody need die because of his battle. He then pilots the TARDIS back to the church, which has returned to Earth, and as Ace wakes, he places the essence of Qataka’s life within the baby. Peter and Emily will raise her as their own, and will name her Ishtar.

As soon as the Doctor has recovered, he and Ace clean up the loose ends from the battle. In a laboratory in the future, genetically blank babies are being grown without sensory input for use as experimental subjects; the Doctor kidnaps one and takes it back to the church to drop it off with Emily. He then takes Ace back to Perivale, where she stops Chad from killing her younger self. Having done this, she recalls that Chad grew up, sorted himself out and got a good job -- at least, he did now. The Doctor and Ace depart for new adventures, as Trelaw buries the head of Lieutenant Hemmings and ponders the lesson which the Doctor has learned -- a lesson which his old hermit mentor taught him long ago, and which it seems he finally understands.