The parishioners of Cheldon Bonniface walk to church on the Sunday before Christmas, 1992. Snow is in the air, or is it the threat of something else? The Reverend Trelaw has a premonition, too, and discusses it with the spirit that inhabits his church. Perhaps the Doctor is about to visit them again?
Some years earlier, in a playground in Perivale, Chad Boyle picks up a half-brick. He's going to get that creepy Dorothy who says she wants to be an astronaut. The weapon falls, splitting Dorothy's skull. She dies instantly.
The Doctor has pursued the Timewyrm from prehistoric Mesopotamia to Nazi Germany, and then to the end of the universe. He has tracked down the creature again: but what trans-temporal trap has the Timewyrm prepared for their final confrontation?
Early in young Dorothy McShane's life (or Dotty, as she is called) a young boy named Chad Boyle picks up a brick on the playground and hits her in the head with it, killing her instantly. Some time later, now awaiting trial and remanded to his mother's care, he is spirited away by a man in a police box. Elsewhere (and probably elsewhen, though still in modern times), in the village of Cheldon Bonniface, there is a church…and it's alive. Or rather, it's permanently inhabited by an energy being named Saul, who doesn't really even know his own origin. With the reverend Ernest Trelaw, Saul is a force for good in his community, and suddenly, he is faced with an odd couple. Peter Hutchings is a mathematician of considerable skill; his wife Emily is a scholar of music, and unknown to her, possesses a strong psychic ability. They cannot have children; and so Emily is stunned when, during a service, the Doctor runs in and places a baby in her hands, then runs back out.
Ace is disturbed. The Doctor has been acting strange, leaving the TARDIS at night in random places, setting up future gambits, but something is not right about it. Now, they travel to Cheldon Bonniface, but in the Victorian era, where the Doctor is known. Ace is attacked by a child-sized astronaut, and runs away and finds herself on the moon. The astronaut is revealed to be her childhood bully, Chad Boyle; he sends her mind away and places her body in the church, but Saul is not present in this time. Meanwhile the Doctor realises the entire village is a fake, and meets with an old adversary, Lieutenant Hemmings of the Freikorps (last seen in Timewyrm: Exodus, boarding a TARDIS). Hemmings, controlled by the Timewyrm, fails to capture the Doctor, who escapes in his TARDIS. The Timewyrm inhabits Boyle's body, and kills Hemmings, sending his mind to the same place as Ace's.
Ace, she finds, is in Hell. Or so it is portrayed, anyway; she has her doubts. Some things are inconsistent: A library, a peaceful flower garden, and a strange room with thirteen stalls, six of which are filled with indeterminate, but humanoid, forms. Something claiming to be her rational side (but in fact is the Timewyrm) uses her to unleash a massive amount of power, vaporizing the real-world Cheldon Bonniface and all its people, and yanking the church (with Saul, Trelaw, the Hutchings, and the baby still inside) to the surface of the moon. Ace's body appears inside the church as well, on the altar, still alive but without her mind inside. The Doctor arrives inside the church, as does the Timewyrm, who forces him to confront a specter of death; but he is not moved. The Doctor enlists the help of Trelaw, Saul, and the Hutchings (leaving Emily in particular with a strange amulet) and then allows the Timewyrm to send his mind to the same place as Ace's, leaving his body in the church. The Timewyrm itself then abandons Boyle's body and follows the Doctor in.
Ace meets the Librarian, an old man who shows her that it is not Hell after all. Rather, it's the interior landscape of a mind that the Timewyrm has occupied as a base of operations. The Doctor joins her, and rescues her from torment; he learns that she is vacillating between maturity and childhood, and realises that it is because of the conflict between himself and the Timewyrm. If the Timewyrm wins, then, among other things, the vision of Chad Boyle killing Dorothy will come true, eliminating her entire adult life. If the Doctor wins, time will be restored. But the Doctor is losing.
Ace and the Doctor are confronted by the Doctor's personal demons — the ghosts of many who have fallen in service to him. Leading the pack are three of the Doctor's former companions: Katarina, Sara Kingdom, and Adric, all of whom gave their lives in service to the Doctor. The Doctor and Ace escape this vision, and are captured by Hemmings, who is torturing a prisoner. He threatens the Doctor, who gives up Ace to be tortured instead, but this allows him to confer with the prisoner. The Prisoner admits that he failed to resist Hemmings because he was troubled by his own demons. They join minds and send a message to the group in the church.
Together, Emily, Peter, and Saul interpret the message, which leads them to recover Hemmings' severed head from the moon. They are able to force Hemmings' consciousness back into the head, removing him from the internal landscape and freeing Ace, and letting Hemmings finally die for real. This allows the Doctor and the Third Doctor to escape imprisonment. They meet a cryptic ferryman, who takes them to the area around the mindscape's central pit. Ace, now caught in illusions of the idyllic life she wanted as a child, eventually frees herself and joins the Doctor; the Third Doctor turns back to monitor her progress.
At the pit, Chad Boyle confronts them, and stabs the Doctor — a mortal wound, but he will be slow in dying. Ace drives Boyle off, and helps the Doctor down to the bridge over the pit. She confronts the Timewyrm, which reveals its plan: this is not just any mindscape, but the Doctor's, where she hid herself long ago in Mesopotamia. As well, she has been able to exercise control briefly on several occasions, and has used the Doctor and the TARDIS to set the pieces of this complex plan in place; hence, the Doctor's mysterious nighttime excursions. If she can destroy the Doctor here, she will take over his body and powers, and consume the universe. Meanwhile, the group in the church, still following the Doctor's message, are stunned when the amulet opens into a portal into the Time Vortex. Working together, they find a path leading to the Doctor and Ace, and Emily goes through to rescue them. She successfully brings out the Doctor, but Ace is trapped. Ace is confronted by the dead companions again, who tell her to go into the pit and free the Doctor's conscience. She finds it in the form of the Doctor's incarnation two regenerations ago, tied to a tree; she frees him, restoring the Doctor's conscience. Enraged, the Timewyrm attacks her, and Chad Boyle as well.
Outside, the Doctor has the power now to crush the Timewyrm; but doing so will kill Ace as well. With his conscience restored, he cannot do that. He pilots the TARDIS into his own inner landscape, and confronts the Timewyrm there, and offers it not death, but peace. In terror, it destroys Chad Boyle to unleash its full power on the Doctor. He locates the humanity inside, Qataka, the woman it once was, and offers it peace. Qataka agrees, and he absorbs her into himself. The Timewyrm's power, now a facet of the universe itself, becomes dormant. The Doctor and Ace return to the church, and he releases Qataka's essence into the baby, which the Hutchings will now raise and name Ishtar. Qataka will have her chance at redemption.
The Doctor and Ace return the church to Earth, where the explosion never happened, now that the Timewyrm is removed. They spend some time wrapping up loose ends, obtaining the baby from a lab and placing it with Emily, stopping the childhood version of Chad Boyle from killing childhood Ace [and realizing that Chad turns out well in the end], and finally, departing. Trelaw, meanwhile, buries Hemmings' head, and pondering the outcome of it all.
- The Doctor
- Chad Boyle
- Emily Hutchings
- Peter Hutchings
- Ernest Trelaw
- K'anpo Rimpoche
- Anthony Rupert Hemmings
- The Doctor feels immense guilt over the deaths of Katarina, Sara Kingdom and Adric.
- The Doctor makes the sign of the Horns of Rassilon with his fingers.
The Doctors as they appear within the Seventh Doctor's mind
- The First Doctor is the librarian and keeper of the gardens.
- The Seventh Doctor is sometimes terrified of the Third Doctor. He is haunted by the realisation that the Leader of the British Republic was his counterpart.
- The Fourth Doctor is the ferryman.
- The Fifth Doctor is enchained in the pit, but is freed by Ace. He is the Doctor's conscience.
- Johnny Chess was reviewed in the NME - 18th July 1998.
- Ace's fear of clowns is mentioned, as well as her having a lock of Cheetah Person fur in her jacket.
- Shreela and Midge are thought of and there is a vague reference to Manisha, Ace's friend whom she mentioned when she was at Gabriel Chase.
- The essence of the Timewyrm is placed in a baby by the Doctor and given to Emily and Peter Hutchings, with the name Ishtar Hutchings.
- Peter Hutchings is a Cambridge University Mathematics professor.
- The Doctor mentions having met Sherlock Holmes.
- Ace is a fan of the Happy Mondays.
- Emily Hutchings is mildly telepathic.
- Saul pushes Hemmings' head along the surface of the moon through telekinesis alone.
- This is the final novel in the Timewyrm tetralogy.
- Paul Cornell based much of Timewyrm: Revelation on a short story called "Total Eclipse":
In its original form as 'Total Eclipse', it was the last of a trilogy concerning Saul the sentient church, and two time travellers from a dictatorial future who'd come back to 'fix' the past, with the Fifth Doctor, Tegan and Nyssa getting in the way. (Said Cornell, "They were the TARDIS crew I wrote mostly for.")
- The name Mount Cadon was invented here. It has been referenced in several other stories.
- Russell T Davies would praise the book in an interview, mentioning that "Paul bloody Cornell gave us Doctor Who, but he made it real. I mean, real people, laid bare, exposing all their anger, passion, and, damn it, nobility." 
- Cheldon Bonniface is the location of Bernice Summerfield and Jason Kane's wedding on 24 April 2010. (PROSE: Happy Endings)
- The reasons why the Sixth Doctor does not make an appearance are revealed in PROSE: Head Games.
- The Timewyrm claims to have been around during the events of TV: The Daleks' Master Plan, Earthshock, Ghost Light, and The Curse of Fenric.
- Lt Hemmings last appeared in PROSE: Timewyrm: Exodus and puts in an appearance in Happy Endings.
- The Doctor recalls his second incarnation meeting him in a dream. (PROSE: Timewyrm: Apocalypse)
- The Discontinuity Guide to: Timewyrm: Revelation at The Whoniverse
- The Cloister Library: Timewyrm: Revelation
- Bewildering Reference Guide entry for Timewyrm: Revelation, with notes by the author
- A Conversation with Paul Cornell by David Bishop (Interview) - TSV 28
- Paul Cornell by Paul Scoones (Interview) - TSV 48