Many years later, after many adventures, Romana -- now in her second incarnation -- has become the President of Gallifrey. She is working to make it a more liberal and open society, and to this end, she has convinced the High Council to change the planet’s oldest laws and open up the Academy to students from other worlds. CIA Co-ordinator Narvin, whose job is to ensure Gallifrey’s security, is losing sleep over the thought of so many aliens running loose on his world -- and Inquisitor Darkel, whose position is becoming redundant due to Romana’s liberal policies, also believes that this gesture is a step too far. Narvin remains loyal to the office of the President, despite his personal feelings about Romana, but Darkel advises him to be sure which side he’s on. By changing Gallifrey’s most ancient laws, Romana has shown her enemies that it’s possible to change the laws that keep her in power -- and Darkel is now watching and waiting for her moment to bring down this liberal President.

Romana visits the cells to speak with the sole prisoner, Andred, and Castellan Wynter, an inexperienced new recruit from the Arcalian chapter, insists upon accompanying her. Andred has been locked up for over six weeks, ever since the revelation about his regeneration, and although he claims to have purged all trace of Torvald’s personality from his system, he still disapproves of Romana’s policies and shows some sympathy for the Free Time movement. He’s also bitter that Leela hasn’t spoken to him since they returned to Gallifrey. Romana dismisses Wynter and speaks privately with Andred, trying to determine whether he can be rehabilitated; however, he refuses to tell her what he knows about Free Time unless she agrees to exile him from Gallifrey so he can have his freedom in the outer Universe. She refuses, convinced that he’d try to raise an army with which to depose her, thus embarrassing Gallifrey once again before the other temporal powers. Romana leaves Andred in his cell, warning him that he’ll stay there until he co-operates. Some time later, Darkel visits him as well, to discuss her plans to remove Romana from office and overturn her liberal policies. She needs to know if Andred can be trusted, and since he spent so much time pretending to be Torvald immediately after his regeneration, that means he never had a chance to let his own personality reassert itself. Andred insists that it was the real Torvald, not him, who had a connection to Free Time, but Darkel still feels he could be a dangerous liability.

Leela remains bitter about Andred’s betrayal, and, seeking solitude, she and her K9 unit have descended into the Vaults: the abandoned areas of the old Capitol, now home to power couplings, the occasional water reservoir and at least one fluctuating access point to the Matrix. Leela feels that Andred’s regeneration has forever changed the man she loved, but K9 assures her that his confusion will pass -- and she’ll never know when unless she speaks to him. A disembodied female voice suddenly speaks to Leela, addressing her by name and claiming that it has a job for her. Leela, wary, agrees to listen to the voice’s offer, intending to play along and learn all she can before reporting back to Romana. But as she steps forward to address the voice, she vanishes into thin air, and the voice breaks out into mocking laughter...

Cardinal Braxiatel addresses the new students at the Academy, both Gallifreyan and otherwise, assuring them that as their chancellor, his door is always open to them. His speech puts most of the students at ease, but Romana is upset that Braxiatel referred to himself as Chancellor, a post that has been empty for some time. They have argued about this before; Braxiatel claims that he could better serve Romana better on the High Council, but Romana refuses to give her political enemies further ammunition by appointing a close friend to one of the highest positions on the planet. If people such as Narvin or Darkel were given cause to look into Braxiatel’s past, they might discover that he’s in constant communication with his own past and future selves, all of whom are supplying a future version of himself with alien artefacts for his Collection. The public scandal could ruin all that Romana and Braxiatel have worked for. Braxiatel concedes the point and stops pressing Romana for the appointment... but that may be because she casually referred to herself as the Ice Maiden, a reminder of the past that worries him for some reason.

Narvin summons Wynter to discuss co-ordinating their work, but Wynter has no interest in working alongside the CIA. Narvin insists that they both wish to protect and serve Gallifrey, but Wynter’s first loyalties are to President Romana, who appointed him to his position despite his lack of practical experience. Narvin wearily dismisses Wynter, realising that the naive young Castellan doesn’t appreciate that the Chancellery Guard and CIA will have to work together in order to clean up the mess that Romana will leave behind her. He then visits Andred in the cells, just to make it clear that he has no use whatsoever for the disgraced Castellan. Darkel has suggested that Narvin let Andred work for the CIA, but Narvin hasn’t forgiven Andred for killing Torvald and doesn’t trust him an inch. Andred notes that Narvin seems tired, but Narvin blames it on stress and leaves Andred locked up in the cells.

Romana’s K9 unit receives word from his twin that Leela has vanished, and Romana takes Wynter to the Vaults to investigate. They find only K9 Mark I, who simply repeats the words “Pandora, Imperiatrix” whenever K9-II speaks to him. Romana recognises the title Imperiatrix, which is what Mephistopheles Arkadian called her when they first met -- but she has the impression that she knew it even before that. Wynter takes K9-I back to Braxiatel for repairs while Romana and K9-II search for Leela, but on his way back into the Capitol, he runs into Narvin. Narvin notes with some interest that Romana has turned to her friend Braxiatel to repair K9, when there are any number of other Time Lords equally qualified to do so. As Braxiatel acquires more and more responsibility and power in the Capitol, it may only be a matter of time before Romana decides that her Castellans are no longer necessary -- and though the Castellans’ positions are protected by ancient laws, Romana has changed some of those laws already. Narvin returns to his duties, leaving the worried Wynter to ponder his warning.

Romana experiences a strange sensation, as if she’s just been scanned by a security system, and she and K9-II then find the missing Leela, who claims to have been contacted by an evil spirit. Romana is irritated that Leela is again seeking irrational explanations for rational events, at least until the voice speaks to her as well, greeting her as Lady Romanadvoratrelundar of the House of Heartshaven -- and suggesting that “President” is a lowly title for one who should be known as Imperiatrix. K9 now announces that he’s tracked down information on the title of Imperiatrix; the first female President of Gallifrey, Pandora, took the title and tried to overturn the ancient laws set down by Rassilon. The voice is surprised to learn that Romana and Leela have met Rassilon before, hidden in a separate partition of the Matrix, and Leela and Romana realise that the voice does not know as much as it would like them to believe.

Meanwhile, someone kills the guard on Andred’s cell and releases him, giving him access codes for the APC Net and instructions to search its data banks for information on Pandora. Andred agrees to his rescuer’s terms and visits the Archives, where he presents the elderly Archivist with a letter of authority granting him permission to act as an important Time Lord’s research assistant. The Archivist, unable to follow the constantly changing politics within the Capitol, accepts the letter as legitimate and grants Andred access to a research terminal. Andred looks up the data, with the Archivist helpfully commenting on the legends that have sprung up around the reign of the Imperiatrix -- but once Andred has found all he needs, he shoots and kills the Archivist.

According to the legends, Pandora decided to lead Gallifrey to war, using the power of time travel to reshape the web of Time to her own design. To this intent, she took an offworld bodyguard, possibly Killoran, who killed all those who opposed Pandora’s will. The High Council eventually convinced Pandora’s bodyguard to betray her by promising to use their control over history to improve her people’s lot; however, once Pandora was in custody, they sent the bodyguard back home and placed her planet in an eternal 6.8-second time loop from which there was no escape. Pandora was then dispersed, executed so thoroughly that she never existed in the first place -- which is why she only exists in legend, not history. The dispersal chamber was located somewhere in the old Capitol, which was destroyed in Gallifrey’s civil war; the new Capitol was built over the ruins, which are now the Vaults. The legends say that Pandora’s dying scream still echoes through the Vaults, vowing revenge...

Leela is disturbed by the parallels between the legends of Pandora and Romana’s own Presidency, but though Romana insists that she is not the Imperiatrix reborn, Pandora reminds her that she’s seen herself as Imperiatrix in a Matrix projection. Romana then realises that the sensation she experienced earlier was the result of stepping through a Matrix door; she, Leela and K9-II are no longer inside the Vaults, but within a Matrix partition where Pandora’s spirit survived. Romana still insists that she controls her own destiny, but Pandora reminds her that, after vowing never to return to Gallifrey, Romana returned from E-Space, accepted the position of President, appointed an alien bodyguard and set about overturning Rassilon’s ancient laws. Like it or not, Romana carries the Imperiatrix Imprimatur... and Pandora claims that Romana accepted that imprint into herself by choice.

As Wynter is trying to explain why he allowed the President to wander off alone into the Vaults, Braxiatel receives word that Andred has escaped and an Archivist has been killed. Narvin -- who is growing increasingly tired, as he hasn’t slept in four days -- summons Darkel to the scene of the crime in case an Inquisitor is needed; however, when Wynter looks up the codes used to access the terminal next to the body, he finds that the codes in question are Narvin’s. Braxiatel unexpectedly speaks up on Narvin’s behalf, as he feels it’s obvious that whoever set Andred free also supplied him with Narvin’s codes in order to leave a false trail; in any case, he’s also realised why Narvin is suffering from sleep deprivation, and feels that this is a more important matter to deal with. As Wynter prepares to organise the search for Andred, Darkel leaves to consult with the other Inquisitors, realising that she’s underestimated her opponents; despite their mutual loathing, Braxiatel would not see Narvin condemned for a crime he hadn’t committed, while Narvin remains loyal to the office of the President despite hating the woman who currently holds it. Darkel still believes that she could get Narvin on her side, however, if she finds a way to put a different President in office...

Down in the Vaults, Leela, Romana and K9-II are shown a projection of the past, in which young Romana’s first incarnation met Pandora in the Vaults and was offered a chance to gain ultimate power over the Time Lords. Leela is surprised to learn that her friend is not in her first body, and questions why she regenerated when there was no apparent need. Romana had always claimed that this was due to vanity, but her first incarnation -- or rather, the Matrix projection of her -- turns on her future self and accuses Romana-II of figuratively murdering her, Romana-I, by forcing an unnecessary regeneration upon herself. As the two Romanas argue, however, Pandora apparently vanishes, presumably having been distracted by events elsewhere -- and the Romanas drop the charade, assuring the confused Leela that they are on the same side and were only pretending to be enemies in order to keep Pandora off guard.

While K9 monitors the carrier waves that indicate Pandora’s presence, Romana-I explains that she confessed everything to Braxiatel after she met Pandora in the Vaults, and that he hypnotised her in order to block her memory of the encounter. This is why Romana-II does not desire to be Imperiatrix, and why she doesn’t recall having been tutored by Braxiatel; as far as she was knew, she first met him after she returned to Gallifrey, when he sought her out and offered to help her political campaign. The two Romanas now realise that Braxiatel was caught off guard when the White Guardian sent Romana with the Doctor to collect the Key to Time. During the course of her travels, she was tortured by an agent of the Black Guardian, the White’s equal and opposite -- a being of almost unlimited power. This trauma may have broken her hypnotic conditioning and uncovered the Imperiatrix Imprimatur, and if so, she presumably forced her own regeneration in order to scramble up her memories and bury the genetic link to Pandora once again. Unfortunately, K9 now discovers that Pandora never left after all; she’s been listening to everything, and she now dismisses the projection of Romana-I, having learned all she needs to seize control of Romana-II’s body through the Imprimatur and rule Gallifrey as Imperiatrix once more.

Braxiatel and Narvin head into the Vaults, and on the way, Braxiatel tells Narvin what happened to Romana as a young student. Since Narvin is likely to be charged with murder unless he can defend himself, Braxiatel reluctantly takes Narvin into his confidence, swears him to secrecy, and admits that he’s in regular contact with his past and future selves; it was a future self, more adept at hypnotism, who put the blocks in Romana’s memory to protect her from the Imperiatrix. Narvin realises that Romana must know that Braxiatel has broken the laws of Time, which is how she got the information she needed to protect herself during the inquiry into the Free Time threat. He promises to keep his word and their secret, but he now understands why Braxiatel made such an effort to seek out Romana and aid her campaign when she returned to Gallifrey. He hadn’t predicted that she would leave the planet with the Doctor, and wanted to keep her under his watchful eye... and perhaps under his control.

Romana now understands that Pandora has manipulated her genetic heritage in order to create the perfect host for the Imperiatrix’s will -- and she is apparently considering the opportunities that this power would offer her. As Imperiatrix, she could reshape Time to her own design, put an end to Free Time and the petty politics of the Time Lord hierarchy, and restore Andred as Leela knew and loved him. Aware that Narvin and Braxiatel have arrived and are listening to her, she nevertheless suggests that she and Pandora are thinking along the same wavelengths. K9 understands what she really means, and when the furious Narvin turns on Romana, refusing to let her turn Gallifrey into a dictatorship, K9 catches him off-guard, stuns him, and simultaneously closes down this Matrix partition, using the frequency of the carrier wave he detected while monitoring Pandora. Pandora is locked away once again, and Romana, Leela, K9 and the unconscious Narvin are returned to the Vaults.