The TARDIS materialises on the planet Pakha, and the man once known as the Doctor -- and now as the Valeyard -- sends his companion Ellie Martin to collect the legendary Ancient Diadem, an object of great and terrible power. He is no longer the same man who once let that power slip through his fingers -- and if Ellie fails to collect the Diadem, he makes it very clear that he will abandon her here. As Ellie scales the cliff, using canisters of greganic acid to carve footholds and handholds in the rock, a Pakhar arrives to investigate the intrusion into the sacred cavern and is shocked to find two aliens trying to steal the Diadem. He is even more shocked to see that the aliens have arrived in the legendary TARDIS. The Valeyard promises to explain everything -- but as soon as the trusting Pakhar is within reach, the Valeyard snaps his neck. Ellie takes the death in her stride, but is surprised that the legendary Doctor could be so ruthless. But as he’s said before, the Valeyard isn’t really the Doctor any more.

On the space station where the Sixth Doctor was placed on trial, Mel is speaking with the Time Lords’ new President-Elect and Co-ordinator Vansell of the Celestial Intervention Agency. The corrupt High Council has been deposed, and the Earth has been put back in its proper position in time and space. However, the Doctor has been lost; as the Fantasy Factory exploded, he rushed back to save his nemesis, and both he and the Valeyard were trapped as the Matrix collapsed around them. Nobody is quite sure what happened to the Doctor next -- and, to Mel’s consternation, Vansell admits that they don’t actually want to rescue him. It has been known for a Time Lord on the point of a regeneration to be visited by an inchoate form of their future self, but it is unprecedented for an amalgamation of their future life essences to be given actual, independent existence. If the Valeyard does defeat the Doctor in battle, he will have access to all of the Doctor’s past and future experiences and memories, and, as such, Vansell considers him a fascinating object of study.

Mel, appalled, points out that the Valeyard they knew was a composite of the dark sides of the Doctor’s personality. What might he do if let loose, unchecked by the Doctor’s morality? Vansell assures her that the Valeyard and the Doctor are still locked in battle elsewhere in the Matrix, and in the meantime, he, Mel and the President-Elect can still use the Matrix to observe possible projections from the future, just as the Doctor presented a sequence from his own future during his trial. The three enter the Matrix through the Seventh Door to access the projection of the Vervoid adventure -- but see that, this time around, it was the Valeyard and Ellie Martin who boarded the Hyperion III. And this time around, the Valeyard didn’t think of using vionesium against the Vervoids until it was too late, and every human being aboard the ship was slaughtered -- apart from the Valeyard and Ellie, who decided to cut their losses and flee, leaving the ship full of Vervoids en route for Earth.

Mel is appalled by what she’s seen, and puzzled by her own absence. When Vansell checks the Matrix records, he finds that Mel apparently never left Earth with the Doctor; instead, she remained in Brighton and eventually died of a brain tumour caused by overuse of a cell phone. When Vansell uses the Matrix to access the day Mel met the Doctor, they see the Valeyard send Ellie to intercept Mel just outside the Brighton police station, delaying her for a few vital seconds so that she never actually meets the Sixth Doctor. The Valeyard has just changed an aspect of his own past -- and his conversation with Ellie reveals that he’s also helped the Thals to wipe out the Daleks before they ever got out of their bunker. He is confident that, if it proves necessary, he can always go back in time to change things back the way they were.

The President-Elect is beginning to doubt the wisdom of letting the Valeyard run free, and Mel agrees; the Valeyard seems interested in creating chaos for its own sake. However, Vansell points out that the Time Lords themselves once sent the Doctor on a mission to destroy the Daleks, and he failed. Perhaps the Valeyard, rid of the Doctor’s spurious morality, may be more useful to the CIA. Vansell decides to watch a few more Matrix projections, and sees the Valeyard and Ellie visiting a Silurian bunker in the Galapagos islands. There, the Valeyard repairs the bunker’s alarm clock so the Silurians will wake on schedule; perhaps when the human race evolves, the Silurian civilisation will be there to welcome them, and humanity will have spaceflight by the time of the Roman Empire. When Ellie questions the wisdom of the Valeyard’s actions, he threatens to take her back where he found her -- about to be run down by a police car while protesting a highway extension. He graphically describes the agony she’ll suffer in the accident, and she is suitably cowed and stops referring to him as “the Doctor.” Satisfied, the Valeyard takes her away, once again certain that he can always return to put the Silurians back to sleep if the need arises.

Mel has seen enough, and the President-Elect is having grave doubts about letting the Valeyard run free, but as they argue with Vansell, something terrible happens to the Matrix. When Vansell investigates, he finds that both Gallifrey and the space station have been destroyed; the Matrix is decaying, and within 60 years there will be nothing left. Vansell traces the cause to the planet Uxarius, in the year 1471 -- and sees that the Valeyard shot his way past the Primitives guarding the Doomsday Weapon and turned it on the constellation of Kasterborous. Now he’s rid himself of the interfering Time Lords, and acquired the ultimate weapon; he once foolishly rejected its power, but now he will be able to use it as a threat to force all those in the Universe to bend to his will.

Vansell has learned his folly too late. While they were watching projections of the possible future, the Valeyard defeated the Doctor and took on the Doctor’s future incarnations as his own. Now only the Valeyard is left, and with Gallifrey gone, Vansell doesn’t have the power to go back in time and change the outcome of their fight. Mel, convinced that the Doctor’s spirit survives somewhere within the man he’s become, offers to try to reason with him. The President reluctantly offers up his personal Time Ring, and Vansell provides Mel with a staser pistol and sends her on her way. She is Gallifrey’s last hope; if she can’t defeat the Valeyard, then the Time Lords will never have existed.

The Valeyard has decided to move the Doomsday Weapon into his TARDIS, but to do so he needs to reconfigure the interior of his ship. Thus, he requires the help of the mathemeticians of Logopolis, but unfortunately that planet was destroyed when the Fourth Doctor inadvertently took the Master there. The Valeyard decides to materialise his TARDIS in the path of its past self, knocking the Fourth Doctor off course and preventing the sequence of events that led to the destruction of Logopolis. However, something goes terribly wrong. Despite his careful calculations, the Valeyard inadvertently Time Rams his past self’s TARDIS and destroys it. The energy wave vapourises Logopolis, kick-starting the end of the Universe, but that’s small potatoes to the Valeyard, who is far more concerned with the fact that he’s just killed his past self -- thus making his own existence a temporal paradox...

In the dungeons of Chronopolis, Mel speaks with Nula, who informs her that the dungeons contain one representative of every species capable of time travel, and that the rest of their species were eradicated by the Mighty One. Nula is from the planet Archetryx, and her fellow prisoners included an Urbankan (until he was shot trying to escape) and one of the Monan Host. Gerrof was the last of the Tharils, and by killing him to make a point, Mel has eradicated an entire species. She’s depressed to realise how little she cares; the things she’s seen since starting this mission have changed her, and not for the better. Nula is stunned when Mel casually admits that the Time Lords were the Mighty One’s first victims; when Mel arrived with her staser and her Time Ring, Nula believed that a Time Lord had finally come to save them. Most of their fellow prisoners have been beaten down and will not help Mel to fight her way out of the dungeons, but Nula offers to accompany her. The dungeons are guarded by the Moroks, the only race of time-travellers to survive their encounter with the Mighty One -- because they surrendered to him and now serve as his private army. This time, when the guards arrive to hand out the prisoners’ rations, Mel guns them down.

The Valeyard tries to save himself by travelling back in time and warning his past self not to travel to Logopolis, but a build-up of time distortion prevents his TARDIS from materialising properly. He tries to shout out a warning to his past self, but due to the time distortion, his past self only hears part of the warning -- and the mention of Logopolis inspires him to travel there in the first place. Frustrated, the Valeyard returns to his TARDIS, and warns Ellie that she too is in danger; the web of Time is trying to repair the damage he’s done to it by erasing him from history, and if that happens then she will never meet him and will suffer the consequences.

Desperate to put things right, the Valeyard decides to travel back even further in time and use the Doomsday Weapon to destroy Logopolis before his fourth incarnation’s visit, thus ensuring that his fourth incarnation never actually travels there and is not accidentally killed. He thus returns to Uxarius and destroys Logopolis, but just as he’s beginning to relax, he begins to feel unwell again. The obvious occurs to Ellie: the Fourth Doctor was paying a return visit to Logopolis, and the web of time is trying to unravel the Valeyard from history. What if, through sheer coincidence, the Valeyard destroyed the planet Logopolis at the very moment that his earliest self was visiting it for the first time? Ellie helps to get the unstable Valeyard back into the TARDIS, and although he seems to recover once he is outside the space/time continuum, he finds that there are now gaps in his memory. Ellie starts searching for one of the Doctor’s diaries, hoping to find evidence to support her theory -- and perhaps some way to solve the problem before she and the Valeyard vanish completely.

In another era, on a slave ship heading for Chronopolis, two slaves named Nula and Gerrof are surprised to find that one of the new prisoners appears to be human. They’ve seen a de-horned Nimon and heard rumours that a Navarino had been captured, but they’d believed that the human species had been wiped out. The new prisoner, Mel, claims that she walked up to a building she knew the Mighty One to be in and demanded an audience with him, only to end up here. When she sees the city of Chronopolis laid out before her, she recognises it as proof that the Mighty One is who she thinks he is. It’s made of crystal and appears unpopulated, but in all other respects it’s a replica of her home, Brighton.

In one of the Doctor’s old diaries, Ellie finds the entry she’s looking for; it seems that the First Doctor, Steven and Dodo visited Logopolis shortly after leaving the city of Kiev in the 13th century. The Valeyard must find a way to stop the First Doctor from visiting Logopolis, but as he tries to come up with a plan, Mel materialises inside the TARDIS, direct from the remains of the Matrix. She tries to speak to the man she knows as the Doctor, but he rebuffs her, insisting that the Doctor no longer exists. The Valeyard is a new man, one who intends to recover all of the weapons of mass destruction which the old Doctor would have buried away or destroyed, and use them to create a new realm in which he is the absolute ruler. But first he has more immediate concerns, and he thus intends to travel back to Kiev and kill Dodo -- using a knife which once belonged to an “artist” in Whitechapel -- in order to prevent his first incarnation from setting off to Logopolis on a pleasure jaunt. Mel can’t believe that the Doctor would do such a terrible thing... and the Valeyard thus takes the knife and casually murders Ellie, partly so he can focus on his own problems without distraction but mainly to prove to Mel that he’s not the man she knows. He then takes the Time Ring from the horrified Mel, damages it, and expels her from his TARDIS, sending her spinning off helplessly into the Time Vortex.

This is the beginning of Mel’s long quest to track down the Doctor again, which finally ends up in Chronopolis with Nula by her side. There, Mel shoots her way into the Mighty One’s throne room, but it takes some time for him to recognise her. He remembers her at last, but can’t remember how she died; she could have died on Earth in the year 2012, or on the colony world of Heritage, or when the spaceship Nosferatu II crashed. But Mel is no longer the trusting and somewhat naïve woman he knew; she’s seen the havoc which the Valeyard has wrought throughout space and time, and knows that there’s no reasoning with him any longer. He really isn’t the Doctor; the Doctor always knew better than to go for the easy solution.

The Valeyard scoffs at Mel, and at Nula, who fears him yet still believes that there’s hope. Mel also believes that the presence of the prisoners is proof that the Valeyard retains some small measure of the Doctor’s morality, as he’s been keeping alive one survivor from each of the species he’s destroyed. The Valeyard scoffs and pronounces himself the lord of creation and destruction; Chronopolis is located at the very heart of the space/time vortex, and from here, he can travel through interstitial time and create or destroy at a whim. He demonstrates his power by stabbing Nula five years in the past, then snapping her neck seconds before she enters the throne room, and then restoring her to life. Mel has had enough; she’s given the Doctor a chance to assert himself, and it hasn’t happened, so she shoots the Valeyard. But he travels seconds back in time and removed the gun from her hands before she has the chance to shoot. As he laughs triumphantly, however, everything around them begins to disintegrate -- the throne room, Nula, and even the Valeyard himself seem to vanish into a void...

Mel suddenly finds herself standing in the console room of the TARDIS -- and the real Valeyard is cowering in the corner, literally afraid to move. Chronopolis has vanished like the phantom it was; the TARDIS was using the last dregs of its energy to generate possibility projections, to keep the Valeyard safe from himself. The quivering Valeyard reveals that he’s travelled back and forth through time, meeting his past and future selves, changing his own past and the past of the Universe so many times that he no longer knows what, if anything, is real. All the Valeyard ever wanted was to be real himself, but when he got the chance, he squandered it by wantonly destroying other possibilities. The changes he made cascaded through Time until he could no longer keep track of them himself, and his only choice was to hide away inside the TARDIS, protected by the illusion of an impenetrable fortress which would keep everyone out. Chronopolis only resembled Brighton to Mel because the Valeyard had made it in the image of his home, and when Mel arrived she saw it as her own home.