The year is 2981. Someone is enlisting discredited but loyal soldiers for a secret army, and an underground resistance movement against the cruelty of the Earth Empire has found unexpected help. While the war with the Ogrons drags on longer than anybody had expected, Leabie Forrester, head of the ultra-rich and powerful Forrester family, is still trying to find some trace of her missing sister Roz. But the Doctor has other concerns; an expedition to the planet Iphigenia has found something it shouldn't, and the Doctor must stop a follow-up expedition from getting their hands on it. The Doctor takes Chris to sort out fo the problem, but leaves Roz in the human colony Fury on Aegistus to sort out a side-effect, explaining that he can't let her come into contact with the artefact on Iphigenia -- her life has too many possibilities. Roz eventually locates her target, a member of the original Iphigenia expedition who has been possessed by an N-form; realizing that Roz has discovered it, the N-form pursues her through the city, but she has laid her plans well in advance and tricks it into materializing under a million-ton slab of dwarfstar alloy, crushing it out of existence. When she returns to her hotel room she discovers that it's been searched, but before she can investigate, she has a vision of an alternate timeline's Doctor, who informs her that things have gone out of control on Iphegenia.

The Doctor and Chris accompany Professor Martinique's follow-up expedition to Iphigenia, but Chris believes any follow-up should have been military in nature, and suspects that Martinique's student Iaomnet is in fact an undercover security officer. When the ship passes over the site of the Iphigenia artefact, the student Emil Zatopek, a latent psi, experiences a strong psychic backlash; nevertheless, he accompanies the others to the site to find out what caused it. Shortly after the expedition enters the site of the artefact, an explosion of alternate realities sweeps through the ship, and soon afterwards Martinique arrives, carrying the delirious Doctor. The Doctor recovers and orders Chris to take him to Cassandra, the outermost body of the star system, immediately.

Iaomnet has also survived -- and has also rescued the Doctor, although it takes him some time to sort out which of the timelines he now remembers really happened. Roz arrives to rescue them, having used her family name to convince the captain of the Wilfred Owen that she is on a secret mission for the Empress, and the Doctor orders her to take him to Cassandra. There, Iaomnet accompanies them into the heart of Cassandra, which appears to be a giant comet -- but which is in fact an ancient TARDIS, damaged and abandoned during the war with the Vampires. The TARDIS has been sending a distress signal which is drifting through Time and Space, randomly activating any N-forms it encounters. The Doctor programmes it to self-destruct.

Chris, Martinique and the Doctor are captured arrested by the crew of the starship Victoria, but before they can arrest the others on Cassandra, the Victoria's captain deliberately allows the crew of the ship Claremont to board his ship and seize control of it for the secret army. The Victoria is damaged when Cassandra explodes, much to the Doctor's surprise, as he'd been planning to destroy it himself. When the Wilfred Owen arrives with another Doctor on board, the Doctors realize that the one who arrived here with Chris is from an alternate timeline, brought into existence by the reality explosion on Iphigenia. The Ogron engineers from Chris' ship give their lives to hold off pursuit by Imperial forces while the Doctor repairs the Victoria's engines; they are also working for the leader of the secret army, who has promised to free the Ogrons from slavery once in power.

The Doctor orders that Iphigenia be placed off limits, and returns to Earth to pick up his TARDIS, which he'd left behind so it wouldn't be affected by its proximity to Iphigenia. On the way back, however, the alternate Doctor remembers that he is Zatopek, who was transformed into a copy of the Doctor by his proximity to the reality explosion. Zatopek helps Iaomnet to kidnap the real Doctor, but Iaomnet then abandons Zatopek and takes the Doctor to Imperial Intelligence for questioning. Roz and Chris, unable to locate Iaomnet, decide to trail Zatopek instead, and follow him to the Temple of the Adjudicators on Tethys. There, they are attacked by psychic assassins, but are saved by Roz and the Doctor's old friend FLORANCE. As they escape, Roz is confronted by the man who searched her rooms on Aegistus, and he introduces himself as an agent of her sister's; Leabie has finally managed to track her down.

Upon learning of the Doctor's presence, the Empress invites him to a private meeting. She is over a hundred years old, is slaved to the computers which run the Earth Empire, and wants only to die. Having put together fragments of records from the past century, she has learned who the Doctor is, and as an independent agent with nothing to gain, only he can grant her the freedom she desires. He does so, but is arrested and charged with regicide. At his trial, the assembled peers unexpectedly transform into monsters and attack the Duke Walid, one of those next in line for the Imperial throne. The Doctor saves Walid's life, and Walid invites the Doctor to help investigate the attack. Everyone who was transformed had latent psi genes, and none of them survived the changes to their bodies. However it was done, the obvious suspect is Walid's rival for the throne, the Duke Armand.

Walid takes the Doctor to a meeting with Leabie Forrester, where the Doctor, reunited with Chris and Roz, explains what happened on Iphigenia. During the war with the Vampires, the Time Lords placed early warning devices on the ancient ley lines of the Universe; one such Nexus exists on Iphigenia, and the Doctor accidentally triggered it by getting too close. Zatopek is an agent of the Brotherhood, which seeks control of this wellspring of psi power; they have made a deal with Duke Armand, who has agreed to help them if they make him the new Emperor. More latent psis in Walid and Leabie's entourages are transformed into monsters, and although Walid survives the attack some of Roz's young cousins are killed. Furious, she demands that the Doctor help her track down whoever is responsible.

The investigation leads the Doctor, Roz and Chris to Armand, but they find that the Brotherhood has abandoned him as a lost cause and gone to ground. Zatopek has also been abandoned, and is dying, since the alternate-Doctor which latched onto him does not exist in this Universe. Zatopek tells the Doctor that the Brotherhood will soon achieve its dreams of liberation, but dies without giving him any further details. Armand is arrested by Imperial Intelligence, and Walid bcomes the new Emperor and appoints Roz Pontifex Saecularis of the Guild of Adjudicators. Roz pledges to clean up corruption in the Guild, and appoints Chris the new Lord High Sheriff of Earth. The Doctor doesn't believe that all has been resolved, however, and accepts an invitation from Walid to discuss the Brotherhood.

Chris accompanies the Doctor to the meeting, where they learn that Walid has also been dealing with the Brotherhood, who switched allegiances when they decided Armand was not going to succeed. Iaomnet and Martinique have been interrogated and their minds erased, their bodies now serving as shells for the gestalt intelligence that is the Brotherhood's Grandmaster. The Doctor realizes that there is another Nexus in the Earth's solar system, and the Brotherhood intend to use it to change reality and release the hidden psi potential of the entire human race -- whether they like it or not. But the possibilities released by the Nexus are random, and they need the Doctor to help them control the changes. As the Nexus passes through conjunction, the Brotherhood attempt to force the Doctor into parallel timelines, seeking one alternate who will tell them what they need to know. Chris, however, also changes -- to be replaced by a telepathic Pontifex Saecularis who rescues the Doctor from Walid.

Roz pilots the Doctor and Chris back to the Forrester home, and before the conjunction ends and reality returns to normal, the telepathic Chris and the Doctor come up with an emergency plan. The Doctor then prepares to set off in search of the Nexus, but before he can go, Leabie reveals that she is the leader of the secret army. She has promised to clean up the corrupt Empire and make a better life for everyone, but first she must deal with Walid, and she needs Roz to keep the Adjudicators out of the fight. Roz, blaming Walid for her young cousins' deaths, agrees to help Leabie, despite the Doctor's objections; they're here to fight a threat from outside linear Time, and if Roz chooses to step back into history he won't be able to help her.

The Doctor and Chris locate the Nexus on Mimas, a moon of Saturn, but they are captured by the Grandmaster, now a gestalt entity residing in several bodies. Following the N-form attack in 1987 and their encounters with the Doctor throughout history, the Grandmaster has become convinced that human psis can only protect themselves through strength in numbers. Thus, the Brotherhood has devoted centuries of research and experimentation to find a way to turn the entire human race psychic, and now they intend to do so with the Nexus. The Doctor, however, reveals himself to be another alternate; the real Doctor was hidden inside the Nexus by himself and the telepathic Chris before the last conjunction ended. He now emerges, triggering another reality explosion. Just as happened to Zatopek, the Grandmaster's bodies are overwhelmed by alternate timelines which latch onto them -- and in all of those alternatives, the Doctor has died. The Grandmaster's bodies die and vanish, putting an end to the Brotherhood.

Roz plays her part and orders the Adjudicators to stand down as Leabie's army attacks Walid's forces; but she refuses to stand on the sidelines while others die in a war she helped to start, and forces her reluctant sister to send her into the front lines. The Doctor, who has just emerged from the Nexus in which all possible futures can be seen, knows that he's too late to save her; Roz participates in the final attack on the heavily defended dome where Walid is hiding, and is killed.

Leabie becomes the new Empress and vows to keep her promises to clean up the corrupt Empire. The Doctor suffers a heart attack at Roz's funeral, and has a vision of Death; despite his constant efforts to cheat her, he has been unable to prevent her from taking his companions, and she will soon take him when he is alone and friendless; without warning, and without meaning. The Doctor sinks into despair, and even a visit to Benny and Chris can't cheer him up; but Kadiatu Lethbridge-Stewart then arrives and orders him to snap out of it. He can't just sit back and do nothing; despite his best efforts, Roz wrote the last chapter of her life by herself, and now it's up to him to decide what will happen next to him.