Ancient Gallifrey is a matriarchy ruled by the Pythia, an absolute tyrant with the power to see into the future -- but the future which once seemed so secure is slipping from her grasp as Rassilon and his neo-technologists threaten her authority with a new age of science and reason. Her one hope of holding onto power is an angry young man named Vael, one of the few Individuals who can block out the communal thoughts of his fellow Gallifreyans. Insecure and filled with bitterness towards those who do not recognise his born greatness, he does not apply himself to his studies and thus fails his assessments. In a fit of rage he turns the full force of his mind on a fellow student, incinerating her. The Pythia learns of Vael’s powers and brings him under her patronage, intending to teach him to control his rage and groom him to become her successor. Under her guidance, Vael infiltrates Rassilon’s followers and joins a team of time-travelling pioneers, but he does not feel welcomed by them and eventually his rage gets the better of him once again. During a test run he lashes out in anger at the child Pilot, breaking the communion between the team and sending their Time Scaphe veering out of control, lost in time and heading for a collision with the future -- a blue box with a flashing light on top.

The Doctor and Ace are having lunch on Ealing Broadway when reality begins to distort around them. A silver cat leads them back to the TARDIS, which is in serious trouble and is planting illusions in their heads to draw them inside; however, for some reason it has removed its door, and they are unable to enter. When two policemen arrive in response to complaints about the Doctor’s odd behaviour, he gives them his UNIT pass and orders them to call the ID number on it. When they do so, the phone in the police box rings, and when the Doctor reaches out and answers it without looking, he and Ace are transported directly into the TARDIS. There, they realise that an alien parasite is caught between the inner and outer doors, and is trying to get inside. The Doctor dematerialises, intending to deposit the creature somewhere out of harm’s way, but the TARDIS stalls in mid-flight and the lights go out. The ship’s dimensional interface has been breached, and that includes the dimension of Time; thus, the parasite has already broken into the ship even though it has not done so yet, and it is leeching power and data out of the TARDIS’ structure. The Doctor sets off to find the parasite and do battle with it, but before he can locate it the power drain becomes critical. A grey, unmarked sheet slides out of the console and is deposited into Ace’s hands, and before she can get it to the Doctor, the dying TARDIS collides with the out-of-control Time Scaphe -- and both ships are destroyed.

Ace awakens in a dusty grey City, where she finds a slime trail similar to the one left by the parasite in the TARDIS -- but this one is a hundred times larger. Exploring further, she sees the former crew of the Time Scaphe surrounded by red-helmeted guards and threatened by the traitor Vael. Vael orders them to search the haunted sector of the City for the stolen Future, and when they refuse, he arrogantly crosses the border himself, unleashing a psychic storm which drives the Phazels and their guards away. Ace is then contacted by a young man named Shonnzi, who seems to know both her and the Doctor already, but rather than tell her about the Doctor he takes her to his home and tells her to hide while he summons the Phazels. Once they are all together, Shonnzi has Pekkary tell the story of their arrival in the City, and Pekkary recites the oft-told tale about their ship, betrayed from within and attacked from without. Stranded in this City and enslaved to the Process, they seek the Future which the cruel Doctor stole from it at the Beginning of the World.

Ace emerges from hiding to tell them that they’ve got it all wrong, and in so doing, changes the pattern of Time across the City. The Process detects this disruption to its carefully ordered Now, and blames Vael for failing to secure the Future. Vael, fearing its reprisals, sets off to find Shonnzi and reclaim his master’s favour, while the Process sends its guards to find and dispose of the unwanted alternative. The Phazels, meanwhile, are upset to see Ace, whom they have already encountered, but when she guesses that they are from Gallifrey, the name of their forgotten homeworld opens up the floodgates of memories in their minds. The guards arrive, but the Phazels allow Ace to escape, unwilling to make the same mistake twice. Ace flees into the haunted sector -- where she sees the ghost of the Doctor. Shonnzi tells her that the Doctor’s ghost entrusted him with its memories, but even though the Phazels claimed he was destroyed at the Beginning of the world, she still refuses to accept that he is dead. Shonnzi and Ace split up to avoid the approaching guards, but Shonnzi is captured by Vael and taken to the monstrous Watch Tower in the centre of the City. Ace, fleeing, reaches a mercury stream on the border between two Phases of the City -- and is forced to cross it when the Process, a giant leech with mouths on both ends of its body, approaches her along the banks of the stream.

Elsewhere, it is earlier, and the Chronauts have only just arrived. Suffering from telepathic shock over the loss of their Scaphe, they watch as the Doctor, searching for some sign of Ace or his TARDIS, instead encounters a younger version of the leech creature and recognises it for what it is -- the parasite which invaded his TARDIS and gorged itself to bloating, destroying his home in the process and stranding him in a warped, desolate city without a future. He is forced to retreat before the approaching monster, but falls into the mercury river and is swept downstream to his apparent death. The Chronauts remain in a state of shock -- all but Vael the Individual, who turns them over to the Process as slaves in exchange for priveleges as their overseer. From this day forth they will be Phazels, bound to search the Phases of the City for the Future stolen by the Doctor. Ace then arrives, and, seeing younger versions of the people she has just met, she realises that by crossing the mercury stream she has somehow gone back in Time. These Phazels, newly arrived, still believe that she and the Doctor attacked them, and when Vael arrives, seeking the source of the disruption which has so unnerved the Process, they turn her over to him. They ignore her warnings that she has seen their future -- and that if they don’t help her, they will be enslaved to the Process forever.

Ancient Gallifrey is in upheaval as the Pythia awaits the return of her successor. Against the advice of his mysterious advisor, Rassilon visits the Pythia to taunt her, predicting an end to her empire of superstition. The Pythia can no longer see the Future clearly; her visions show her only a wall guarded by Rassilon and his cronies, beyond which she cannot see. Without Vael, the Future which she had planned out has been stolen from her. She retreats into a world of her own, waiting for Vael to return, but as she withdraws from public life, support for Rassilon and his followers begins to grow.

As Vael and the guards drag Ace to the Watch Tower, Vael explains that the Process has planned out all of Creation from the Beginning, and will not tolerate any alternatives. At the Tower, the young Process prepares to dispose of Ace, but is interrupted by the arrival of its elder self -- the one which Ace fled from earlier, which has come back to find out why the past is no longer as it remembers. The younger Process has failed to protect its Now, and the Future they seek has slipped further from their grasp. As the Processes argue, the Doctor’s ghost appears before them, distracting them while Ace escapes. The silver cat reappears and leads her to the summit of the Tower, where she sees that the City is divided into three Phases, all of which curve upwards on the interior of a vast sphere. She also finds and frees Shonnzi from a silk cocoon, but Vael attempts to recapture them, and as they retreat the silver cat trips Ace up, causing her to fall from the Tower. Her fall is cushioned by a force field, as is Shonnzi’s when he leaps after her, and she realises that the TARDIS must be nearby, protecting them both.

Guided by the glowing TARDIS key, Ace locates an attic doorway which she recognises from the TARDIS. Inside, the Doctor is apparently waiting for her, but when she speaks to him she finds that his memories have gone -- or have been taken from him. She takes him outside to meet the waiting Phazels, the elder versions whose memories of Gallifrey have been restored; they now understand that he means them no harm and may be the only one who can save them. But with his memory gone, the Doctor has no idea where to start. Vael reappears and tries to recapture them all, but Reogus impulsively challenges the guards -- and when he is accidentally killed, one of the guards vanishes into thin air. As the guards scatter in terror, the Doctor orders them to tell the Process that Will Be has arrived to challenge Now for control of the City -- but he privately admits to Ace that his challenge was premature, and that he still does not understand enough to fight the Processes effectively.

The Process’s Now is no longer recognisable, but the young Process ignores the warnings of its elder self, insisting that the changes are merely omens of the Future they seek. When the old Process protests, its younger self drives it out, claiming that the elder’s world has failed, and that the younger shall create a new Now. The old Process, realising that its foolish young self is about to destroy everything they have worked for, burrows beneath the City to reclaim its birthright and start Now all over again from the Beginning.

As the Phazels consider the implications of Reogus’ fate, Shonnzi and Ace confront the helpless Doctor, but he is clearly out of his depth. The cat therefore reappears, transforms into the Doctor’s ghost, and restores the real Doctor’s memories. The cat and ghost are manifestations of the TARDIS Banshee Circuits, a final desperate cry for help which has taken on the form of the dying ship’s owner. Shonnzi realises that it was not the Doctor who entrusted him with his memories, but the TARDIS itself which was merely using him as backup storage. Once she is sure that the Doctor is back to his old self, Ace gives him the TARDIS greyprints, which the Doctor uses to access the flight recorder through the Banshee Circuits. Thus the truth is finally revealed -- the City itself is the TARDIS, turned inside out by the Process. Already damaged, and straining to control the energies released by the interaction of three different time zones, its last dregs of power are now being drained by the new Beginning set in motion by the elder Process. The TARDIS took away the Doctor’s memories to keep them from the Process, but it has now returned them out of desperation -- for if the Doctor fails and the TARDIS dies, everything and everyone within the City will be destroyed.

The Pythia grows ever more irrational as the Future slips from her grasp, and to his shame, Rassilon realises that his spiteful taunting is largely responsible for her breakdown. The Pythia sends her loyal followers to steal the eye of a Sphinx, a foreseer killed by the Hero Prydonius, in the hope that it will restore her power to see the Future. Desperate to find Vael, she gouges out her own eye and puts that of the Sphinx in its place. Transported by pain and vision, she sees that her Future lies outside everything she has ever known, in a self-contained world which was meant to last forever but is growing smaller by the minute…

Now that he knows himself to be inside his TARDIS, shaped into an ancient Gallifreyan city by the artron energy of the Chronauts, the Doctor accesses its Architectural Configuration and reshapes the walls of a nearby building to trap the elder Process upon its return. While he tries to question it, however, the Phazels are drawn away by a psychic call which only Vael the Individual can resist. Desperate to escape the future which has been planned out for him, Vael tells the Doctor that this is the beginning of the final Phase of the City; the Phazels, weakened by their harsh life and unable to resist, will be forced into the beetle uniforms. Once their minds are subsumed by the Process they will be sent back to the earliest Phase to enslave their own younger selves, while the Process eats the elderly, wasted bodies of the spent guards. This Time, however, it will be different -- for the young Process now intends to place control helmets on the young Phazels as well, making all of its Now the same from the Beginning.

The old Process tears itself free from the Doctor’s trap, and the Doctor and Vael are separated from Ace as they flee. The Doctor uses the last dregs of his ship’s power to reconfigure a spiral staircase out of the landscape and relocate it to the Watch Tower, where he intends to confront the Process and reclaim his ship. Vael finally realises that this entire City is the Doctor’s time machine, but the Doctor is unwilling to tell him anything about it; Vael may be able to provide him with answers to questions about Ancient Gallifrey which he has sought all his life, but if he tells Vael too much about his own future he risks altering the past. The Pythia invades Vael’s mind, demanding to know what is happening, but he resists her, asserting his own Individuality. He and the Doctor are then captured by the young Process, who has them taken away to await the Future it has planned for them.

The City is collapsing, its dimensions contracting as something like a moon tears itself free of the sphere opposite the Watch Tower. Ace, fleeing from the old Process, meets the eldest Pekkary; thanks to Ace’s reminder his heritage, he survived his confinement in the beetle helmet, and fled before his younger self could take him to the Tower to be eaten. Together, they cross the mercury stream to the earliest Phase of the City, where Ace confronts the distrustful young Phazels and reminds them of Gallifrey. This restores their memories and reunites them as a crew, but before they can do anything about it they are captured by the guards that they are destined to become, and Ace realises that one of the guards is her own older self. As Now folds in upon itself, the different Phases of the City are grinding together; past and future are becoming one. Only the young Pilot who will one day grow up to be Shonnzi understands that the Process can only be destroyed before its Beginning -- but can he warn the Doctor in time?

The Doctor senses someone looking out at him from Vael’s mind, an elderly woman as desperate to know the future as the Doctor is to understand the past. Despite the risk, he agrees to an exchange of questions, and thus learns that he is speaking to the Pythia, matriarch of Gallifrey -- and is forced to tell her that she will be the last of her kind. The prophecies state that the next ruler of Gallifrey will be a man, but they never said he would be her successor. Ace, meanwhile, slips away from the Phazels while the guards are distracted by the silver cat, but as she tries to find the Doctor one of the guards locates her. Ace defends herself and manages to remove the guard’s helmet, and briefly sees an older, wasted version of herself before the elder Ace staggers away in shock and falls to her death. Stunned, Ace finds and releases the Doctor, who promises to stop that terrible future from happening.

The Doctor takes Ace and Vael to confront the Process, and tells it that Processes go nowhere in an eternal Now with no Future. The young Phazels, once more telepathically united, commune with their future selves and give them the strength to remove their beetle helmets. The old Process then arrives to supervise its own birth, and when the young Pilot identifies the approaching “moon” as a giant egg, the furious young Process attacks and kills its elder self. Vael then reveals that he has the TARDIS key, the key to the Future, taken from the attic doorway in the confusion of the Doctor’s return. He and the Process both try to kill the Doctor at the same time, and when the Process inadvertently drags the Doctor out of the way, Vael’s power blasts the egg to ashes just as the newborn Process begins to hatch. Destroyed before its Beginning, the Process vanishes. Vael, taunted by the Doctor and urged on by the Pythia, loses his temper for the last time. Determined to free himself of the Pythia and make his own future, he turns his power on the eye within his mind -- and incinerates himself.

The end of the Process has made the Phazels a redundant timeline, and they vanish as the young Chronauts, their Time Scaphe restored, return home to Gallifrey. But Gallifrey is now a very different place. The future which once seemed secure now belongs to Rassilon, and the Pythia therefore sends her loyal sisterhood to the planet Karn, curses Rassilon and his followers to a sterile future, and plunges to her death in the abyss beneath her temple. From this day forth no children were born on Gallifrey, and Rassilon and his advisors -- including one whose name has been lost to history -- had to divert their attention away from the time-travel projects in order to secure their race’s future. But the truth of what happened during those dark days has been lost to the past and glossed over by the official histories. In the future, the Doctor is left with nothing but life-long questions to which he may never have the answers -- and a damaged TARDIS in desperate need of repair.