Gallifrey has been plunged into civil war. On the one side is Romana, the rightful President of Gallifrey; on the other is Pandora, the embodiment of all the evil in the Matrix, which has cohered around the personality of a former Imperiatrix of Gallifrey and obtained corporeal form by stealing the biodata of Romana's first incarnation. Pandora's allies include the devious Inquisitor Darkel, the obsequious Chancellor Valyes, and numerous Time Lords who have been forced to do her bidding by a post-regenerative mutagenic virus that has robbed them of their free will. Romana has only a handful of supporters left, including Co-ordinator Narvin and Commander Hallan; most of her guards died defending the alien students whom Romana had invited to attend the Time Lords' Academy before war broke out, and whom Pandora had ordered executed. War fleets from the rival temporal powers are in orbit around Gallifrey, ostensibly out of concern for their students' welfare, while Romana and her surviving supporters are hiding in the Maelstrom Cloisters near the Outlands.

Romana has used her Presidential access codes to scramble the imprimaturs of the TARDISes in the berthing bays, grounding them all and depriving Pandora of the ability to selectively edit the history of this war. K9 has been infected by the dogma virus and now serves Pandora; he has locked Romana and her supporters out of the Matrix, and they are thus unable to keep Pandora under observation. As Romana doesn't have the manpower to fight Pandora directly, she's been forced to destroy parts of the Capitol to rob Pandora of its resources; the archive banks have been razed, destroying millions of years' worth of recorded history, and Narvin and Leela are even now preparing to destroy the artron microforum. These actions are turning even the uninfected against Romana, and she's trying to enlist the help of Gerber, a former commentator for the Public Video Registry who is still respected for his principles. He supports her in spirit, but in practice, there is little he can do. He's working on a vidcast that he hopes will sway hearts and minds back to Romana's side, but while he still believes that it's possible to win the war with reason and hope, Romana fears that those halcyon days are long past...

Narvin and Leela have been sent to destroy the artron microforum, where the excess artron energy from the minds of Time Lords was once absorbed and directed to the berthing bays. Since the TARDISes are now grounded and Gallifrey is at war, the forum is deserted and can be destroyed with no loss of life. But since Pandora has control of the armouries, Romana's supporters have been forced to rely on old, poorly maintained weapons -- and one of the percussion grenades that Narvin and Leela are planting goes off prematurely. Blinded by the blast, Leela nevertheless manages to find her way back to the Cloisters, carrying the grievously injured Narvin with her. Chancellery guard Annos takes Narvin for treatment while Romana and Hallan check Leela's eyes, but Leela has been blinded before, and insists that once her eyes change colour, she'll be fine.

Meanwhile, Pandora's allies have either been robbed of their free will or are serving her for their own devious purposes; she puts her trust only in K9. The guards sent to investigate the explosion at the artron microforum report that the damage is less extensive than expected, and that they've found an unexploded bomb in the rubble. Valyes and Pandora soon realise what's happened, and decide to detonate the second bomb and tell people that the first was planted as a lure to draw innocent victims to their deaths. Valyes points out that this claim will prove more effective if innocent bystanders die in the bombing, as this will convince the people that Romana has turned to monstrous tactics out of her desperation to win the war. Pandora agrees -- and when the guards report finding a trail of blood leading out of the microforum, she sends K9 to track it to its destination, taking her personal retinue of guards -- with orders to take Romana, and only Romana, alive.

Narvin and Leela are both in need of medical attention, and Councillor Matthias suggests sending them to a non-partisan medical station he's heard of in the Outlands. Pandora's guards then attack the Maelstrom Cloisters, and Romana sends Matthias to rally the defences. K9 makes it through the front lines of the battle, but Romana bluffs him into retreating by claiming that the holographic image generator she used to camouflage her hideout is in fact a bomb. She and her close advisors thus escape into the Outlands, where Romana orders Leela and Annos to take Narvin to the medical station; in the meantime, she and Hallan will go on the offensive. Former Castellan Wynter's TARDIS was impounded and locked in the Anomaly Vaults when he took it back into its own personal timeline; cut off from the outside Universe, it would have been unaffected when Romana scrambled the other TARDISes' imprimaturs. If Romana can get into the Vault, she'll have access to the only working TARDIS on the planet.

K9 informs Pandora that Romana has evaded capture, but her psycho-spoor indicates that she has recently been visiting the Pazithi Cloisters. Pandora orders K9 to capture Leela, in the hope that a skilled "interviewer" could turn even the savage against Romana -- and her choice of words reminds Valyes of Gerber, the famous commentator and inhabitant of the Pazithi Cloisters. Pandora sends in Darkel, and Gerber tries to stand up to her until she reveals that she has a copy of the vidcast he was preparing for Romana's benefit. He still has a powerful reputation, but Darkel now intends to use that reputation for Pandora's benefit rather than Romana's. Word of the atrocity at the artron forum is spreading, and even Gerber is starting to wonder whether Romana has resorted to killing the innocent in order to get her point across. What he believes is irrelevant, however, as Darkel intends to force him to help Pandora whether he wants to or not.

Annos, Leela and Narvin run into an ambush on their way to the medical station, but since the guards have orders to take Leela alive, she is able to lure their captain into a trap and kill him. Annos shoots down three of the guards, and the sole survivor makes a run for it; Annos recognises him as Janartis, who went through guard training alongside Annos and who's always been trouble. Leela, frustrated by her inability to see her targets, is forced to rely on Annos to guide her through the unfamiliar Outlands. Narvin stirs briefly to consciousness, but he's still dazed and delirious, and is unable to get a clear warning across when Leela tells him that Romana has gone to the Anomaly Vaults with Hallan. However, she does realise that he's very concerned about what they might encounter inside...

Romana and Hallan are concerned by the lack of guards around the Vaults when they arrive; if Pandora isn't trying to stop them from entering, then they're probably walking into a trap. Romana admits that she doesn't fully understand what keeps the Vaults isolated from the outside world; all she knows is that they are infinitely larger on the inside and contain untold numbers of temporal anomalies. Theorising that the control systems must be controlled with telepathic circuits, she tries thinking about defeating Pandora, and the Vault opens up to reveal a woman hard-wired into the control console of a time machine and surrounded by a honeycomb of cells, each containing a humanoid figure. The woman identifies herself as Aesino and demands to know whether the time has come for her to be released. Hallan is disturbed to note that Aesino is carrying a very dangerous-looking gun, but Romana wonders whether this woman could be the means of destroying Pandora forever.

Annos and Leela reach the medical station with Narvin, only to learn that it's run-down and overrun with pig-rats, that most of the medics are on the verge of deserting, and that the man in charge, Elbon, is a cynical opportunist who is charging for his services. He's delighted to learn that his new patients are the former CIA Co-ordinator and the Presidential bodyguard; they're sure to net him a tidy profit, one way or another. Narvin has recovered enough to understand what's going on, and he offers Elbon his personal eye-scan uplink, which will give Elbon access to all of the technology and files restricted to the CIA. Elbon accepts this as payment, but while Narvin's injuries are relatively easy to heal, Leela's aren't; she was not only affected by the flash of the explosion, but by the discharge of artron energy from the forum's receptors. A Time Lord could absorb this type of energy with no ill effects, but Leela has been blinded permanently. Leela seems to take the news stoically, accepting that the planet has repaid her for the joy she took in destroying its monuments -- but once she's alone, her facade crumbles and she weeps.

K9 reports that Leela is heading for the rogue medical station in the Outlands -- and that Romana is heading for the Anomaly Vault, apparently unaware of what's waiting for her inside. He is still working on undoing the damage Romana did to the TARDISes; Pandora has patched her weapons tech into a Space-Time Visualiser, and once K9's work is done, she will be able to target any location on the planet and beyond. Meanwhile, Darkel has ordered Gerber to record a new propaganda broadcast denouncing Romana as a terrorist and murderer, and has reminded him that more innocents will die if he chooses to back the wrong side. Pandora orders Darkel to take Gerber to the medical station to witness the damage that Romana and her allies are about to inflict upon it, but is interrupted by an alarm from the Anomaly Vaults; Romana has entered, and the secondary shields have been raised, trapping her inside. It seems that the war will soon be over...

Narvin wakes to find Leela sitting with him, and after a moment, he recalls hearing that Romana was on her way to the Anomaly Vaults -- which means that the thing inside could soon get the opportunity to possess a Time Lord President. Pandora's guards then attack the medical station, but since Narvin has paid in advance, Elbon shows him the secret way out. Outside, Gerber watches in horror as Darkel orders the guards to firebomb the station and kill everyone within. She then orders Gerber to address the people of Gallifrey and place the blame for this attack on Romana, but Gerber turns to the ocular probe and announces that Pandora is responsible for the carnage they've witnessed. He then leaps into the flames to die a martyr, taking what would be the only honourable way out if the probes actually had been broadcasting live as he'd been told they were. As it is, Pandora, Valyes and Darkel intend to spin the recorded footage to make it appear as though Romana is responsible for Gerber's death, thus trading on his reputation to destroy Romana's. Not that it matters, for Pandora believes that Romana has effectively defeated herself already and will be driven mad by what she finds in the Anomaly Vaults...

Romana and Hallan question Aesino and study the connections between the time machine and honeycomb, and slowly come to realise that every figure in the stasis cells is a version of Aesino herself, each culled from one second into her predecessor's future. Whenever one version of Aesino is killed, the next version is transported to the same co-ordinates to resume the hunt -- and since she was bred to live for a thousand years, there are billions of her in the cells. As an assassin, she's effectively unstoppable -- and Romana and Hallan now realise that the time machine she's been connected to is all that's left of Wynter's TARDIS, which implies that Narvin knew that she was here. But Aesino is quite mad, and she breaks free of her restraints and chases Romana and Hallan through the Vaults, desperate to be free or to kill them if they will not release her. Romana and Hallan discover that the Vault is now sealed, and when Hallan shoots and kills Aesino, the next version of the assassin materialises in the same spot and resumes the chase...

Elbon is the first to flee the burning hospital, and Leela, Annos and Narvin must follow, though this means abandoning the other patients to the flames. They find K9 waiting for them in the escape tunnel -- but rather than open fire, he reveals that he's fighting against Pandora's conditioning and is here to deliver a warning. Pandora has learned about the assassin in the Anomaly Vaults; when the political situation on Gallifrey began to deteriorate, the CIA hardwired Aesino to the remains of Wynter's TARDIS in order to use her as a weapon. Narvin confirms that Romana is indeed in great danger from the mentally unstable assassin, and K9 gives Leela a powerful transmat unit that used to belong to Braxiatel so she can penetrate the shields around the Vault and rescue Romana. K9 returns to lull Pandora's suspicions and try to bring her down from inside. But as Leela, Narvin and Annos set off for the Vaults, Narvin reveals that there's an even greater threat than the time-fractured assassin inside...

Every time Hallan shoots one Aesino, another appears to take her place. However, Romana realises that since the Anomaly Vault is isolated from the outside Universe, she can connect herself to the remains of Wynter's TARDIS and accelerate Time within the honeycomb; thus, each new version of Aesino will come from 100 years in her future rather than one second, and soon the assassin will run out of replacements. Hallan keeps killing Aesino while Romana returns to the console. Narvin and Leela arrive, and Narvin rushes off to warn Romana of the real danger while Leela helps Hallan to fight Aesino. However, Narvin is too far behind Romana, who has taken Aesino's place in the control throne. Her plan works, and the systems begin skipping over millions of potential Aesino duplicates. To Leela and Hallan, the assassin's future selves start to appear older and older until finally the last version of Aesino dies. However, Hallan has come to realise that the assassin was making it too easy for them, and Aesino dies happy, claiming that her tormenter has a new plaything now. Too late, Hallan and Leela realise that death was the release that Aesino wanted -- and it suddenly starts to seem colder in the Vaults...

Valyes is forced to report that Leela, Narvin and Annos have escaped from the medical station, but Pandora already knows that Leela and Narvin have used a powerful transmat to enter the Anomaly Vaults. She orders K9 to launch a stochal warhead and irradiate the area around the Vault; even if her enemies do manage to emerge, the fallout will kill them within seconds. Unable to delay convincingly, K9 has no choice but to do so. Pandora then tells Valyes the real threat that Romana faces: it takes a living mind to keep the contents of the Vault isolated and stable, and the sentience in question is a being older than Time itself, which the CIA found and broke to their will. Since Romana's existence has been usurped by the rebirth of her previous incarnation, this makes her "current" incarnation a temporal anomaly -- and the sentience in the Vault, mad and lonely, will keep her in the Vault as its plaything while Pandora uses the doctored footage from the medical station to destroy Romana's reputation outside.

Narvin arrives at Aesino's honeycomb too late to warn Romana of the threat, and the creature enters her mind through the stasis-cell interface before she can disconnect herself. The creature thinks like a child, if it thinks at all; its attempts to communicate through the telepathic circuits of Wynter's TARDIS drove Aesino mad, and now the same thing is happening to Romana. Unable to tell the difference between its playthings, the sentience begins to fracture Romana's mind, splintering her through Time into the stasis cells that used to house Aesino -- and if it finds the Presidential codes in Romana's mind, it will be able to access the Matrix, escape from the Vault and warp reality. As Leela and Annos catch up with Narvin, he realises that he can divert the power from the stasis cells into Wynter's TARDIS and cause it to dematerialise; however, the power surge knocks him unconscious, leaving him unable to control the TARDIS' flight. Without an outer plasmic shell to protect them from the Time Winds, the occupants will be torn apart. Only Romana can save them now, but she's still linked to the stasis cells, her mind fractured and splintered by the Anomaly creature's attempt to communicate with her...