Inquisitor Darkel continues to attack Romana on all political fronts, and Romana’s sleep is disturbed by terrible dreams of the future. Forced to pick and choose her battles, she’s given in to the Council’s decision to appoint Valyes, though aware that his attitude is exacerbating the tensions created when the Yevnon student Gillestes was exposed as a Free Time agent. Following Braxiatel’s advice, Romana has appointed Leela as a tutor so she can share her experiences with the students and help the different species to co-exist; however, Leela is having trouble dealing with her husband, Andred, who still claims to love Leela but appears to be working on behalf of Romana’s rivals and enemies. Co-ordinator Narvin then discovers that Romana has been visiting the Archives, and realises that she intends to communicate with Pandora once again; she confirms this, but insists that she is safe now thanks to Braxiatel’s sacrifice. Pandora existed in the past, present and future; since Braxiatel has taken the past and present aspects of Pandora away with him, only the future aspect remains in the Matrix, and it can do nothing but whisper of things to come. Narvin reminds Romana that, in her current form, Pandora embodies all of the evil thoughts of every Time Lord mind that has ever been stored in the Matrix; nevertheless, Romana insists that she will be safe, as K9-II will be the one communicating directly with Pandora, acting as a filter so that Romana will not need to make direct contact. Narvin repeats his objections, but Romana flatly orders him not to interfere.

Barech becomes worried when his fellow Monan student, Carel, goes missing, and fears that, due to her particularly non-Gallifreyan appearance, she has become the target of abuse. While he tries to find out what’s happened to her, Neeloc, Taylor and Galadina attend Leela’s first lecture. Neeloc is impressed by her tales of fighting Sontarans on Gallifrey, but Taylor and Galadina are more interested in discussing Leela’s marriage to Andred and how the Time Lords have responded to an alien savage living amongst them. Leela admits that not all Time Lords are happy with her presence, but points out that, as guardians of great powers, they must be careful; it is up to the students to prove themselves trustworthy and to teach the Time Lords to respect them. Taylor and Galadina doubt that the Time Lords will ever truly accept them as equals, however -- and as the class breaks up, Barech arrives, claiming that Andred and Valyes have accused Carel of conspiring with Gillestes and deported her from Gallifrey. Many other alien students have faced similar accusations, particularly the Monans, who have a long and bitter history with the Time Lords. Appalled, Neeloc insists that he and his friends must stand together to vouch for Carel’s innocence, but Galadina points out that if the Time Lords were truly interested in justice, they would have been given the chance to do so before Carel was sent home in disgrace. Taylor angrily demands to know what Neeloc’s hero, the Doctor, would do in this situation.

Darkel goes public with the news about Carel, insisting that this latest arrest just confirms that the alien presence at the Academy poses a threat to Gallifrey. Romana is frustrated by these developments, which are undoing all of the hard work she’s put into forging diplomatic ties with the other time-active powers. Already, the High Monan is demanding an audience with Romana to explain this latest outrage -- and Romana fears that Darkel’s rampant xenophobia will lead to the civil war of which Romana has dreamed. Meanwhile, Andred suggests to Valyes that he withdraw full Matrix privileges from all non-Gallifreyan students in order to prevent another terrorist incident, something Valyes is all too willing to do; as far as he’s concerned, it was a grave mistake allowing alien students free run of the Academy in the first place. The alien students are angered, especially as Gillestes used stolen Matrix codes in order to commit her crime; revoking student privileges is a meaningless stricture that will do nothing to prevent another such incident. Leela tries to defend Valyes’ decision to her students, but her heart clearly isn’t in it; however, though it sickens her to make compromises in the face of adversity, she advises her students to remain calm and wait for Romana to triumph over her enemies. If the aliens act rashly now, they will only play into the hands of people like Darkel.

Despite Narvin’s protests, Romana orders K9-II to connect to the Matrix and access the Pandora partition. Frustrated, Narvin goes to Darkel, claiming that he suspects that Romana is already under Pandora’s influence. But while he is genuinely concerned for Gallifrey’s security, Darkel is more interested in making political capital by letting Romana engineer her own downfall. Meanwhile, to Neeloc’s distress, Galadina falls in with a group of Phaidon isolationists and decides that she can learn more about other cultures by observing them without direct interaction. Leela finds a party of Nekkistani beating up a Sunari student, but even after she rescues him, the Sunari refuses to identify his attackers. Andred, who was watching the incident, warns Leela that this inter-racial conflict is exactly what Darkel warned would happen, but Leela insists that Darkel’s lies and xenophobia are responsible for creating the tense atmosphere in the first place, and storms off, furious with her former lover and with the compromises she’s been forced to make.

The growing violence at the Academy is creating a rift between Neeloc and his alien friends, who don’t believe that a Time Lord can understand the extent of the hatred they face every day. Barech then reveals that he’s acquired an ancient parchment that will give them access to the Time Lords’ great secrets; if they won’t share them willingly, Barech will take them by force. Appalled, Neeloc accuses Barech of infiltrating the Academy in order to steal the Time Lords’ secrets, and Taylor, stuck in the middle, lashes out at both of them and goes out for a quiet walk to get his head together. Outside, he runs into Andred, who advises him to find the proper outlet for his anger. Andred claims that, despite appearances, he supports Romana’s reforms and is fighting her enemies from within -- and he tells Taylor that if her reforms are to be effective, then those who support her must recognise the right moment to strike.

Elsewhere, Pandora speaks to Romana through K9-II, and confirms that the future is one of civil war; however, she speaks of it cryptically, and though she refers to Romana as Imperiatrix, she does not explain exactly how the war will come about. Romana concludes that Darkel is willing to destroy Gallifrey rather than accept that it must move forward with the changing times; however, if Romana steps down in order to prevent a civil war, then Darkel will become President in her place and erase all of the good work that Romana has tried to accomplish. Her only hope is to somehow reason with her enemies, but Pandora claims that her enemies are beyond reason and can only be silenced. Frustrated, Romana emerges from her consultation to find that the High Monan has contacted Gallifrey again and made certain demands; also, Gillestes has finally broken under interrogation and revealed the true nature of the toxin with which she intended to infect the Time Lords...

Leela is growing ever more frustrated by her inability to rein in the violence at the Academy, and finds herself beginning to doubt the wisdom of allowing so many races to mingle when they have such a shared history of violence. She then receives word that all Monans are being withdrawn from the Academy, but when she confronts Valyes, he reveals that this was the High Monan’s choice. Leela accuses him of driving the Monans away with his harsh and unfair regulations, but he insists that his concern has only ever been for his students’ welfare. She warns him that he’s being used as a pawn by Darkel and Andred to undermine Romana, but he takes offence and reminds her that, as a member of the teaching staff, she too falls under his jurisdiction. Frustrated, Leela then finds that Galadina has abandoned her non-Phaidon friends and is now hanging out exclusively with other Warpsmiths; lines are being drawn between the different races, and as it seems that Romana’s experiment is failing, Valyes announces that all remaining students will be segregated into separate dormitories by species.

Infuriated by this latest pronouncement, Taylor agrees to help Barech find out the secrets hidden in his parchment, but has second thoughts when Barech uses codes that he’d stolen from Neeloc back before Neeloc had a reason to keep them secret. Barech hacks into the Matrix to find deeper security codes, but before he can put his knowledge to use, Andred catches them... and, rather than commenting on their actions, informs Barech that the High Monan has withdrawn all Monan students from Gallifrey for their own safety. Neeloc and Taylor bid Barech farewell as he packs, but Taylor decides not to accompany Barech to the scapheport, which will be teeming with angry Monan students who are likely to unleash their frustrations on any humanoid in the vicinity. Before bidding Taylor goodbye, Barech admits that he enjoyed associating with his non-Monan friends -- and pointedly reminds Taylor that it sometimes takes only one man to change the future.

Gillestes has now revealed that the toxin with which she tried to poison the Time Lords’ reservoir was a mutagen that acts upon the brain, making it susceptible to the beliefs and agenda of the Free Time organisation. The virus lies dormant in the brain until triggered by a regeneration, which means that if Gillestes managed to unleash it by some other means before Andred caught her at the reservoir, then there’s no way of telling how many Time Lords have been infected. Darkel accuses Romana of placing the whole of Gallifrey under threat; idealistic as her intentions may have been, by opening up the Academy to their former enemies, she’s caused the planet to be overrun by terrorists and spies. Darkel gives Romana one last chance to accept her error and expel the aliens from the Academy, and when Romana refuses, Darkel announces that she will take her concerns directly to the public and try to force an election. And if the dogma virus has already spread throughout the Time Lords, the result could be civil war.

Neeloc is set upon in the halls of the Academy and beaten half to death -- by fellow Gallifreyans who accuse him of being a race traitor. When the appalled Taylor visits Neeloc in the infirmary, Andred whispers in the young human’s ear, reminding him that it’s only a matter of time before all alien students are expelled from the planet. If Taylor wants to make his mark, he’ll have to do it soon. Neeloc sees Andred speaking to Taylor, and is disturbed when Taylor refuses to tell him what Andred said. Fearing that Taylor is going to do something foolish, Neeloc confides in Chancellor Valyes that Barech had acquired an ancient parchment revealing the location of the Great Key. Neeloc believes that Taylor intends to use the Key to tap into the Eye of Harmony, but Valyes reminds Neeloc that the Key’s hidden location was revealed to the Doctor during the Sontaran invasion and that it was subsequently moved so no future President could find it. Thus, no ancient parchment could possibly lead Taylor to the Key’s current location -- and whoever provided the parchment to Barech had an entirely different agenda.

Again, Romana consults Pandora through K9-II, demanding to know whether Gillestes succeeded in spreading the dogma virus; however, Pandora can no longer speak of the past, and when asked about the future, she only repeats her prophecy that Romana will find only one way to quell the growing insurgency. Romana is actually tempted by the possibility of declaring herself Imperiatrix and simply sweeping aside all those who disagree with her -- but she knows that she can’t lead Gallifrey into an enlightened future by declaring herself a dictator, and that Pandora is trying to tempt her so that she can achieve power by manifesting herself through Romana. Romana disconnects K9 from the Matrix, vowing that she will face Darkel’s challenge with reason, not force.

Andred runs into Leela outside the infirmary, and points out that the attack on Neeloc proves that the violence is running out of control. He claims that he’s just trying to protect Gallifrey and doesn’t care about the wider political ramifications of his acts -- but Leela reminds him that he once cared deeply about such things, and that if people like Darkel had dictated policy in the past, then he and Leela would never even have met. Andred admits that he doesn’t know what he believes any more, and finally agrees with Leela that the man she loved was lost when he regenerated; however, he insists that he’s trying to be that man once more. Nevertheless, she refuses to advise him, telling him that the man she loved would have known what to do for himself. Andred hurries off to make amends, and despite herself, Leela finds herself hoping that her husband can return to her after all. Meanwhile, Andred heads to the Vaults to find Taylor, having finally decided that he’s made a terrible mistake in supporting Darkel. But before he can find Taylor and stop him from making a tragic mistake, Romana steps out of the shadows -- and kills Andred.

Taylor is following the instructions on the parchment, determined to take a risk for the sake of his friends and make his mark on history. Security has already detected his presence in a forbidden area of the Vaults, but before Narvin can send in guards to arrest him, Darkel arrives and advises Narvin to wait. If they arrest Taylor now, they’ll only have circumstantial evidence against him -- but if they catch him in the act of tampering with the Eye of Harmony, they will have positive proof that Romana’s policies have compromised Gallifrey’s security. Darkel assures the worried Narvin that even if by some miracle Taylor were able to access the Eye, the powers would tear him apart without the artefacts of Rassilon to protect him. Unaware that he’s being used as a sacrificial pawn, Taylor finds his way to a door beneath the Panopticon chamber, steels himself, types in the access code and opens the chamber...