The Third Doctor buries Laika, the Earth’s first space traveller, on the distant planet Quiescia as Sarah watches sympathetically. She knows why he cares so deeply, even if he doesn’t...

Lifetimes later, an old acquaintance of the Doctor’s tries to kill him to avenge an embarrassment he suffered years ago. General Tschike has always held back for fear that the Doctor was truly invulnerable -- but events in the East Indies ReVit Zone, formerly known as Borneo, have proven that this is not the case. The Doctor manages to escape but sets course for Borneo to investigate, and he and Sam materialize in the reconstituted rain forest near what appears to be an ancient city but is in fact a block transfer computation set slightly out of time-phase with the rest of the jungle. There, they are pursued by leopards programmed to kill anyone whose biodata signature is not recognised, but the Doctor manages to find the biodata control unit and adds himself and Sam to the guest list.

The City is the site of a very special auction, and bidders for Mr Qixotl’s Relic are already arriving. Earth’s UNISYC is represented by Colonel Kortez and Lieutenant Bregman, and other representatives include a dead man named Trask, a conceptual entity called the Shift, and Homunculette, a Time Lord from the Doctor’s future. Two representatives arrive to speak for Faction Paradox, a cult which uses Time Lord technology to damage the fabric of causality. The Doctor and Sam arrive at the bidders’ lounge, where Qixotl, clearly horrified to see him, claims that he’s an uninvited guest so nobody else will work out who he is. The Doctor plays along for the moment. But then Homunculette’s sentient TARDIS, Marie, explodes for no apparent reason, torn apart from the inside by her own defensive systems. Homunculette leaps to the conclusion that Faction Paradox is responsible...

Sam finds Bregman suffering from culture shock, and while discussing the Doctor’s theories about biodata, Bregman gets the idea to explore the alien quarters to learn more about what the aliens are like. They enter Faction Paradox’s shrine, but Sam realizes that it’s not part of the ziggarut but a pseudo-TARDIS which runs on voodoo rites. Little Brother Manjuele of the Faction catches Bregman trespassing, and as the ziggarut safety protocols are not active on Faction territory, he is able to overpower her and take a biodata sample from her body. She flees from the shrine in shock, and in that condition falls under the spell of the telepathic call emanating from the Relic. Sam follows her, trying to stop Bregman as she throws herself down flights of stairs to reach the Relic more quickly, to answer a call from the future which only a human can understand.

The Doctor confronts Qixotl, demanding to know what’s so important about the Relic. Qixotl admits that in Homunculette’s time-frame, the Doctor’s future, the Time Lords are fighting a war against an enemy which also has the power of time travel. And they are losing; the Enemy has already cut off much of their past to them, deleting most of the Time Lords’ powerful weapons from history. The Relic is a body which contains unique biodata codes, possibly lost secrets which could tip the balance of power and help them win the war. It is the body of a man who had acquired a particularly colourful reputation before he died. It is, in fact, the Doctor’s body.

The body has taken a strange route to get here. The first major battle of the war took place on the planet Dronid, where Qixotl had been stranded; having heard rumours that the Doctor was on his way to the planet -- and that nobody knew whether the Doctor was on the side of the Time Lords, or of the Enemy -- Qixotl had an idea. After the battle, the Doctor’s body was apparently unearthed from the ruins, and sent into the Vortex by a Faction Paradox cultist who didn’t realize its significance until it was too late. The Relic crashed on Earth in the early 21st century and was taken to the Store, a repository of alien technology kept by the American military. After the Dalek invasion of 2164, human military technology was scattered across the planet, and Homunculette arrived on Earth to collect the Relic, having determined that this was the best point in history in which to do so. But he was too late; the Relic had already been moved, and Homunculette found only an invitation to Qixotl’s auction.

Qixotl tries to explain as little as possible to the Doctor, but he does mention the existence of the Celestis. Since the Enemy is also time-active their existence was not predicted by the Matrix, but certain members of the Time Lords’ Celestial Intervention Agency foretold the war nevertheless and deliberately erased themselves from history, becoming conceptual entities which exist only as ideas in the heads of their followers. The Doctor, growing more and more appalled by the stakes in this auction, is even more horrified when a black spaceship lands on the ziggarut, bringing Qixotl’s last invited guests -- the Daleks. But when they go to greet the new arrivals, they find that a Kroton commander, E-Kobalt, has destroyed the Daleks and come to the auction in their place.

Bregman reaches the Reliquary, and before Sam can stop her she attempts to open the container with the Relic and answer its psychic call. But as soon as she touches it, the vault’s defenses are activated and begin to grow weapons tailored from the biodata patterns of the intruders. Bregman’s poor self-esteem is assaulted; although within the human norm she believes herself to be fat and ugly, and the vault’s weaponry emphasizes this and sends her into a state of self-loathing and despair. Manjuele detects this state of weakness and uses the biodata he stole from her earlier to take over her mind, intending to steal the Relic. Sam, meanwhile, is attacked by babies growing from within flowers but experiences only confusion and disorientation -- because although the embryos have been generated from her biodata, the biodata is somehow wrong...

Qixotl is alerted to the intruders but simply shuts off the alarms and gets on with the auction. The Doctor, however, discovers what’s happened and leaves the others to bid on the Relic while he shuts off the City defenses and rescues Sam. As Sam recovers, the Doctor studies the dying embryos and realizes that somehow Sam possesses two strands of biodata -- one her own, and one of a darker, less perfect, and somehow more real “Sam”. Manjuele arrives in Bregman’s body, but the Doctor realizes what he’s done and links his mind with the dead mind of the Relic to drive Manjuele back into his own body. Sam takes the comatose Bregman to her quarters to watch over her while the Doctor returns to the auction, where Manjuele bursts in, having realized who the Doctor really is. The Doctor in turn reveals Manjuele’s plan to steal the Relic, and this triggers a near-bloodbath as the latent hostility between the bidders explodes in violence.

The Doctor is swept up in the bloodlust, and, finally recognizing Qixotl as a man who betrayed him in a previous incarnation, he begins to throttle him to death -- but at the last moment he realizes what he’s doing. The idea to kill Qixotl must have been implanted in his mind, just as ideas have been implanted in all their minds -- Bregman’s idea to search the aliens’ quarters, Manjuele’s idea to use her to steal the Relic, even Marie’s subconscious activation of her weapons systems. And only the Shift can be responsible. The Doctor shuts down his senses, trapping the Shift within his own mind, and the Shift finally admits that it represents the Enemy. It was created with the same technology that the Celestis used to create themselves -- for some of the Celestis are supporting the Enemy, feeling that they’re more interesting than the Time Lords. Trask is representing the Celestis at this auction; the Celestis, who exist only in the world of ideas, require agents in the real world who have accepted their mark, and have the ability to reanimate such agents after their death. The Doctor, having no way to keep the Shift trapped, is forced to release it, and while he is explaining the situation to the others, it retreats into E-Kobalt’s mind and sends it to await its reinforcements.

Now that the others are aware of what the Shift has done, it can no longer influence their subconscious minds. But the Krotons are already on their way, and the Doctor has switched off the City’s defenses. The others must forget their differences for the moment in order to get the Relic out of the City before the Krotons attack, but they’re too late; the Krotons storm the ziggarut, killing Qixotl and forcing the others to scatter. The Doctor provokes a Kroton into shooting at him and seizes some of the shattered crystal from its harpoon, thus acquiring Kroton biomass which he uses to activate the Faction’s shrine. But he finds the shrine too much for him to control and is trapped in a single split-second of Time, where he has the perfect opportunity to consider what he’s learned about Sam. Somebody or something has rewritten Sam’s biodata, turning her from an ordinary, flawed woman into the perfect companion figure. Did someone try to plant her with the Doctor as a distraction -- or did the Doctor do it himself, unconsciously reaching out into Time and rewriting Sam’s life to provide himself with a new companion?

Marie, slowly conducting repairs to herself, contacts the Doctor and helps him to stabilise the Faction’s shrine. He materializes the shrine around the Kroton Warspear, and E-Kobalt, influenced by the Shift to seize the Relic and destroy all who get in his way, tries to blast his way out before the Shift can stop him. The blast is reflected by the interior of the shrine and destroys the Warspear, and all Krotons within the ziggarut are shattered at the same moment. The Shift retreats into the Doctor’s mind, but this time he is prepared for it and traps it in a prison within his mind. He then sets off to collect the Relic and take it to safety, only to find that the Celestis recorporated Qixotl after his death, in exchange for the Relic. Trask has already taken it back to their home, Mictlan.

The Doctor uses his knowledge of biodata codes to pass through the opening to Mictlan after Trask, and finds Bregman already there, having an out-of-body experience. Mictlan appears to be the worst place in the Universe; to Bregman it is an urban slum, and the castle of the Celestis is a run-down, multi-storey car park. There, the Doctor confronts the servants of the Celestis, who inform him that before the battle of Dronid, his future -- final -- incarnation made a deal; the Celestis agreed not to interfere in events on Dronid, in exchange for the Doctor’s body. There were certain stipulations to the deal, but they aren’t important now; they intend to call in the Doctor’s debt by placing their mark on his body while he is still alive, and deliberately left the aperture open behind Trask so they could trap him on their own territory. They place their mark on his mind and release him and Bregman back into the real Universe. The Doctor is allowed to take the Relic with him, as it is now a temporal paradox and thus useless. Upon returning to the City, however, the Doctor reveals that he has tricked the Celestis; when they reached into his mind they marked the Shift, which has already been marked by the Enemy, and the conflict is tearing it apart. Bregman, however, is feeling much better, having realized that the vast forces she’s seen at work still need ordinary humans to observe them if their battles are to mean anything.