Romana, Braxiatel, Narvin and Wynter meet to discuss the matter of the broken man and whether his TARDIS is from the future or not. Romana doubts that the other temporal powers have the skill to clone a TARDIS, but Narvin points out that this may be possible now that alien students have been invited to attend the Time Lords’ Academy. It’s also possible that the original TARDIS made the journey in the past and that its flight logs were wiped using the same Presidential codes it used to get through the security barriers at Davidia; the codes have since been updated, and Romana gives Wynter the old codes so he can investigate. The subject then shifts to Pandora and the K9 units’ attempt to contain her within the Matrix and analyse the threat she poses. The minds of dead Time Lords are stored within the Matrix so the current generation can draw on their accumulated knowledge, and the dead minds’ aggressive, ambitious impulses are isolated and contained within a separate partition, dominated by the mind of Pandora; however, that partition was breached, perhaps deliberately, allowing Pandora to feed off Narvin’s mental energy and try to possess Romana through the Imperiatrix Imprimatur. The K9s have secured the partition, however, and Romana should now be able to access the Matrix without further risk.

Darkel then arrives to question why she was not informed of the broken man’s arrival, and Narvin and Wynter begin to argue over which of them has jurisdiction here. Narvin claims that this is CIA business because the broken man was infected with an alien mutagen, but Wynter claims that this is a matter of internal security because the broken man is a Time Lord. Romana kicks them both out while she decides who to assign to the case. Darkel reminds Romana that Narvin is a more experienced investigator, but Braxiatel points out that Wynter will not gain experience unless he’s given some responsibility, and Romana agrees. As Darkel departs, dissatisfied, Braxiatel reminds Romana that matters of demarcation could easily be resolved if she were to appoint him as Chancellor, but again she refuses, fearing that her enemies would regard this as nepotism. Before leaving, Braxiatel then informs Romana that one of his Yevnon students, Gillestes, is behaving suspiciously; he suspects that someone has helped her to steal his Matrix access codes, but intends to give her free run for now in order to find out what she intends to do with them. He is unaware that she knows of his suspicions and has advanced her own plans accordingly...

Darkel has taken charge of the hunt for Andred, leaving Wynter free to join Leela in the observation chamber while K9-I examines the broken man’s quarantined body. The broken man has finally succumbed to his injuries and died without regenerating, but K9 points out that there were still a number of ways in which he could have communicated with them, which suggests that his features were destroyed not to silence him but to prevent the Time Lords from recognising him. K9 detects residual artron energy within the dead brain, and Wynter orders him to concentrate on finding a match for the energy signature within the Matrix. Darkel arrives to check on the progress of the investigation, and privately tells Leela that Narvin and Wynter are spending too much time arguing with one another and not enough time on the real problems. Casually, she mentions that these matters could easily be resolved if Romana were to appoint Braxiatel as Chancellor, and Leela decides to suggest this to her friend. Elsewhere, K9-II informs Romana that the Pandora partition has been sealed off, and it is now safe for Romana to access the APC Net once again.

Down in the Vaults, Andred stumbles across Gillestes, who has broken into the pumping station and is about to dump the contents of a vial into the Capitol’s water reservoir. Andred overpowers her and contacts Braxiatel to inform him of the incident, and Braxiatel, though promising not to turn him in, advises him to surrender of his own accord; he can’t run forever, and preventing a terrorist attack will count in his favour. Andred concedes the point and turns himself in when Wynter arrives to arrest Gillestes. Gillestes herself is just a fanatic Free Time agent with little understanding of her organisation’s true aims, but while she does not reveal the nature of the chemical with which she intended to contaminate the Time Lords’ water supply, she does reveal that she used Braxiatel’s Matrix codes to access the Vaults. Wynter reports this to Narvin, who advises him to keep the information to himself until he needs something to use against Braxiatel. He may need it; if Braxiatel does convince Romana to appoint him as Chancellor, he would assume jurisdiction over the Chancellery guard, which would mean that the Castellans’ powers, including Wynter’s would be curtailed.

Leela reports on her progress to Romana, and passes on Darkel’s suggestion that she appoint Braxiatel as Chancellor. Suspicious, Romana speaks to Darkel personally, but the Inquisitor insists that she’s only looking out for Gallifrey’s best interests and that appointing a Chancellor in these troubled times would show people that the Presidency is secure. Since Darkel has been one of her staunchest opponents, Romana assumes that her show of support for Braxiatel means that she really does believe it’s in Gallifrey’s best interests to have Braxiatel as Chancellor. Meanwhile, Leela returns to the isolation chambers, where K9-I has identified the dead Time Lord’s artron energy signature but has dismissed the match as impossible. As K9 sets to work analysing Gillestes’ toxin, Andred arrives and tries to apologise to Leela for his cruel actions, claiming that he was confused after his regeneration and thought that he was acting for the best. Unaware that she was not aging naturally, he thought their time together would be short, and, believing that Narvin was involved in a conspiracy to bring about Gallifrey’s downfall, he acted hastily for Leela’s sake. But Leela storms out on him, convinced that, like all Time Lords, he only acted out of a sense of his own importance.

Darkel visits Wynter to praise his work so far -- and to poison his mind against Braxiatel. She claims that Braxiatel is jealous of Wynter’s power in the Capitol, and that he supported placing Narvin in charge of the investigation into the broken man. Wynter, already worried about Narvin’s earlier comments, agrees that it’s important to show Romana that it would be a mistake to place Braxiatel in a position of power. Darkel thus reminds Wynter of the threat posed by Pandora; if someone were to use Braxiatel’s compromised Matrix access codes to release the creature in a controlled manner, so that it could be recaptured and confined before the situation got out of control, then that someone would have proven Braxiatel’s incompetence. Wynter gives in to temptation, and, using the access codes that Gillestes provided while under interrogation, he opens the Matrix partition and tries to free Pandora. To his surprise, however, the partition is already empty. Elsewhere, K9-II finishes analysing the toxin, but then hears Pandora’s voice in his head and shuts down to purge her infection from his circuitry.

Romana has followed Darkel’s advice and appointed Braxiatel to the post of Chancellor after all, to mixed reactions amongst the Time Lords. As the ceremony begins, Wynter tries to report to Darkel, but she doesn’t seem concerned to learn that Pandora has apparently vanished. Narvin then notices Wynter looking upset, and tells him to cheer up, since he now has friends in high places. Wynter is stunned to learn that it was Darkel who wanted Narvin in charge of the investigation, and Braxiatel who spoke up on Wynter’s behalf. Realising that he’s made a terrible mistake, Wynter returns to the isolation chamber, where Leela finds him talking to himself, convinced that he’s heard someone in the quarantine chamber. He breaks quarantine to investigate, and finds that K9 has shut down. Panic-stricken, he insists that he can hear someone else in the chamber, but as far as Leela can tell, he’s only talking to himself. Concerned, she leaves to fetch help, while Wynter rails against the invisible presence.

Following Braxiatel’s appointment, Narvin reluctantly offers his congratulations -- but refuses to shake the exonerated Andred’s hand. Leela then arrives to warn them all of the incident in the isolation chamber, but on their way to investigate, they find a pair of guards lying dead on the ground -- and Leela catches a glimpse of the broken man walking away under his own power, his wrists dripping blood as if freshly crushed. However, the broken man’s dead body is still in the isolation chamber when they arrive -- and Wynter has gone, K9’s nose laser has been removed, and the flask containing Gillestes’ toxin is in pieces on the floor. K9 powers back up and reveals that his personal memory circuits have been purged; however, he was still recording audio input while conducting self-repairs, and once he has fully powered up, he will be able to replay what happened in the isolation chamber after Leela left.

The dead guards appear to have had their minds ripped out of their bodies, presumably by Pandora. Darkel blames Romana and Braxiatel for the creature’s escape, and when Narvin checks the records, he finds that Braxiatel’s Matrix access codes were indeed used to access the partition. He does not believe that Braxiatel is responsible for freeing the creature, as he knows that Gillestes and Wynter also knew the compromised codes; however, he can’t explain why Wynter, the only one with means and opportunity, would have released the creature. Nevertheless, it’s clear to both him and Braxiatel that Darkel manipulated Romana into putting Braxiatel in a position of power so discrediting him would have a stronger effect on Romana’s Presidency.

Andred and Leela must work together to hunt the broken man through the Vaults, but to Andred’s shock, Braxiatel has appointed Leela as acting Castellan in Wynter’s absence. Leela spots the broken man’s trail, but when they lead a squad of guards in pursuit, the broken man turns on them, speaking with Pandora’s voice. The guards’ stasers have no effect on the hideously injured man, who now has the ability to feed on their darkest thoughts, ripping their very souls out of their bodies. Leela and Andred are forced to retreat as the broken man slaughters their guards, and the shaken Andred reveals that he knows all about Pandora and her powers, thanks to Darkel. Somehow, Darkel learned of Pandora’s existence even before Romana and Leela encountered it in the Vaults, and it was Darkel who released Andred from captivity and helped him evade Wynter’s guards in exchange for his help in researching Pandora’s history. Shaken by his first face-to-face encounter with Pandora’s evil, however, Andred now insists that their top priority must be containing it.

K9-I finishes recharging himself, and reveals that he’s finished analysing Gillestes’ toxin -- and that it’s the same mutagenic compound that was found in the brain of the broken man. He now replays the audio data that he recorded while shut down, and Romana and Braxiatel listen as Wynter enters the chamber and begins speaking to someone; they cannot hear anyone else in the chamber, but they subsequently hear what seem to be the sounds of a struggle. K9 then reveals that he also recorded Wynter’s brainwave patterns, some of which can be converted to audio format; when he does so, Romana and Braxiatel hear the voice of Pandora speaking, and realise that Leela heard nothing because the voice is inside Wynter’s head. Pandora is trying to seize control of Wynter’s body, planning to use him to feed on the greed and ambition of the Time Lords until she’s strong enough to take on Romana. Rather than betray his people and his President, Wynter tries to kill himself by drinking the contents of the flask, only to discover that it is not a poison but a regenerative mutagen -- and too late, he realises that he is destined to become the broken man. Wynter desperately tries to kill himself, shooting himself with K9’s nose laser, crushing his hands in the quarantine chamber’s automatic door and biting out his own tongue so Pandora can’t use him to spread her lies -- but Pandora’s power keeps him alive. Broken and all but mindless, the wreck that was Wynter walks out of the isolation chamber, carrying Pandora’s spirit with it to feed on the ambitions of the Time Lords.

Sickened, Braxiatel vows to stop Pandora, and joins Andred and Leela near the President’s office, Pandora’s ultimate destination. He sends them away to prepare while he confronts Pandora -- but he’s not alone, for Darkel is lurking in the shadows nearby, watching. She accuses Braxiatel of placing himself in a position of power so he can become President once Romana has been discredited, and he admits that this is true; however, he accuses her in turn of using Andred to learn about Pandora and then manipulating Wynter into releasing the creature in order to advance her own plans for power. Pandora arrives in the broken Wynter’s body, and is drawn to the greed and ambition in Braxiatel’s mind -- and Darkel departs, smug, as Pandora begins to feed. However, Braxiatel has planned for this, and has set a part of his mind constantly thinking through the equations that make up the shell of the Matrix partition. Pandora is thus trapped in this part of his mind, unable to escape -- for as long as Braxiatel keeps his guard up. To safeguard against accidents, Braxiatel enters the isolation chamber, which K9 has sealed off from the Matrix.

There is no longer any trace of Pandora in Wynter’s mind, and the broken former Castellan makes his way to the TARDIS bays. On Braxiatel’s instructions, Andred has lifted the guard on the anomalous TARDIS, and Wynter takes it back in Time, using the outdated Presidential codes that he’d been given for his investigation to pass through Davidia’s security barriers and warn his President of the evil he’d let loose. Braxiatel is now containing Pandora in his mind through sheer effort of will, but it can still escape if he lets his guard down; thus, to protect his fellow Time Lords, he must foreswear their company forever. Before leaving Gallifrey, he speaks privately with Romana, advising her to ask Leela to tutor the alien students at the Academy so they will see that off-worlders can learn to live in harmony with Gallifreyans. He also warns Romana that Pandora exists in three aspects; he has trapped her past and present within his mind, but her future still exists within the Matrix. Romana is disappointed to learn that her friend has been manipulating her all along in order to become President himself, but he’s paid a terrible price for it, and she agrees to let him keep his title of Chancellor in his self-imposed exile.