Exiled from the Capitol, former President Romana returns to her ancestral home of Heartshaven, but the aftermath of war has left it deserted, dusty and overrun with pig-rats. The only person in the house is another exile -- and it takes Romana some time to recognise the disgraced Janartis, who sought shelter in the abandoned House after Narvin banished him to the Outlands. Starving and filthy, Janartis threatens to feed Romana to the pig-rats unless she agrees to keep him "company" in the House, but as he advances, Leela and K9 arrive in search of Romana, and since Leela is blind, it is K9 who guns Janartis down. K9 assures Romana that his nose laser was set to stun, but Janartis has been weakened by hunger and exposure, and even the stun setting is enough to kill him. Before Romana's eyes, Janartis regenerates -- into a shambling zombie chanting the slogan "Free Time." K9 is forced to shoot him again, this time with maximum force, and Janartis bursts into flames and staggers backwards into the tinderbox that the House of Heartshaven has become. Romana is forced to abandon her ancestral home to the fire, but has no time to mourn its loss, for Janartis' fate indicates that the original dogma virus has broken out on Gallifrey -- in which case, the Time Lords face the greatest threat of their existence.
Gallifrey is struggling to restore its status and reputation in the aftermath of war, and it doesn't help that President Matthias began his rule with the accidental destruction of the Sunari and Nekkistani battle fleets. Matthias has thus been forced to strike a deal with the shady Mephistopheles Arkadian, much to Narvin's disgust, but since most of the CIA's records were destroyed during the war, he can present no concrete evidence that Arkadian is not to be trusted. Matthias dismisses him to deal with matters of lower priority, but instead, Narvin contacts Castellan Annos, who has been assigned to hunt down and exterminate the packs of pig-rats infesting the Capitol. It's a dirty and dangerous job, and Annos himself is bitten by a pig-rat while organising his men; but Narvin has a new task for him, as he needs Annos to fetch the only evidence on Gallifrey that will support Narvin's claims. Meanwhile, Arkadian himself shares a glass of wine and discusses terms; Matthias' offers of reconstruction contracts and mining rights are all very well, but what Arkadian claims to be really interested in are the stockpiles of temporal weaponry that Pandora had accumulated during the war...
Leela smuggles the disgraced Romana into Elbon's medical station by disguising her as an injured patient, but Romana is appalled when Elbon seems to dismiss her warnings about the dogma virus. Furious, she reminds him that Commander Hallan placed himself in temporal quarantine to prevent Pandora's variant of the virus from escaping, but his sacrifice will have been for nothing if the original version, brewed up by the terrorist Gillestes, has escaped. Elbon waits out Romana's tirade and then explains that he's already aware of the situation; he has three regenerated zombies penned up in a quarantine chamber, and he's been running tests on them. K9 identifies the victims as being from all walks of Gallifreyan society, with no apparent common factors, which means that the vector for infection could be anything. Annos then arrives to fetch Leela, who has been expecting Narvin to revoke her position as the Presidential bodyguard and is surprised to learn that he in fact wants her to address the High Council. Elbon orders Annos to arrest Romana, but Annos decides that since she's not allowed to enter the inner Capitol, then logically she can't be there. He thus departs with Leela, and the frustrated Elbon has no choice but to accept Romana's and K9's help with his research into the dogma virus.
Matthias allows Arkadian to address the High Council, and the trader assures the wary Time Lords that he intends to dispose of the temporal weapons under the aegis of an impartial inspection team. Once the weapons have been decommissioned, Arkadian can sell the active by-products, such as taranium ore, for a profit. Valyes suggests just chucking the whole lot at the Daleks, but Arkadian points out that, not only is Gallifrey in dire need of cash, but the presence of dangerous temporal weapons is a serious treaty violation that could lead to yet another devastating war if discovered. Additionally, Pandora didn't consider long-term storage issues when stockpiling the weapons, and they've already begun to decay, risking the stability of not only Gallifrey but the Time Vortex itself. Matthias thus requests that the High Council allow him to open negotiations with Arkadian, but before they can do so, Narvin announces that he's found a witness willing to testify to Arkadian's character, or lack thereof. Leela enters the Council chambers, unsure why she's been summoned -- until she hears Arkadian's voice...
Romana soon realises that Elbon knows more about the infection than he's telling her, and thus orders K9 to burn a hole in the plexi-glass and let the zombies out. Elbon soon realises that she's not bluffing, and admits that the zombies all seem to be shambling off to the catacombs for some reason. Romana takes K9 to see for herself, unaware that Elbon has left out one vital fact: the catacombs are under martial law and any guard patrols she encounters are likely to shoot at any movement. Romana finds this out the hard way when she and K9 stumble across a guard patrol led by Henzil, and as they retreat from the guards they stumble across the lair of the zombies. Thousands of infected Gallifreyans are shambling through the catacombs, chanting "Free Time" and building a gigantic structure out of scrap metal. The number of zombies leads K9 to conclude that at least 35% of the population has been infected, and that the numbers are growing. He and Romana also note that the structure the zombies are building resembles a giant pig-rat nest, and they realise that the zombies are imitating the pig-rats' behaviour -- because the pig-rats are the carriers of the virus. Since Romana is surrounded by pig-rats and threatened by zombies, she has little choice but to call out to Henzil for help.
Leela eventually has to be dragged out of the Council chambers, still giving her opinion of Arkadian at the top of her voice. Valyes dismisses her testimony as unreliable, and Matthias confirms that her visa application will soon be up for review; nevertheless, the Council votes not to deal with Arkadian. Arkadian takes the result with surprising equanimity, and Narvin realises that there must be a catch. Indeed, Arkadian now reveals to the High Council that the dogma virus has broken out. Gillestes bred the virus in a pair of experimental pig-rats, and although she was prevented from releasing the virus in the reservoir, her pig-rats escaped from the student labs when the Academy was destroyed during the war. The infection has been spreading ever since, and Matthias knows it, which is why he'd detailed so many guards to eliminate the pig-rats; but it's been a losing battle, and since Gallifrey's population has been decimated by the war, they have no trained biochemists capable of devising a cure. With the Time Lords' very existence on the line, whoever can provide them with a cure can name their price... and the appalled Narvin realises that the man with the cure is Arkadian.
Afterwards, Matthias and Narvin discuss matters in the Presidential suite; from here, the President can see the entire Capitol dwarfed by the slops of Mount Caden, and understand just how small and fragile it really is. The deal has been made; Pandora's weapons will be transported to a secret location and there traded for the cure, but both Matthias and Narvin fear that Arkadian in fact intends to deliver the weapons to Free Time. They'll need to send Elbon to test the cure, but they'll also need to send along someone cunning, smart, and expendable. At this moment, Henzil brings in the captive Romana, who is surprised when Matthias and Narvin announce that they've got a job for her. Despite her personal issues with Matthias, she listens to the plan, and agrees with Narvin and Matthias that this is no doubt a trap engineered by Free Time. Narvin then reveals that the weapons consignment has been rigged to explode once the deal has been made; if all goes well, Free Time will no longer exist, but the Time Lords will have acquired the cure for the dogma virus. If Romana oversees this mission, Narvin is willing to let her take a TARDIS and leave Gallifrey to travel as a renegade. As there's nothing left for her on Gallifrey, she has little choice but to accept the offer.
Leela visits her husband's grave in the Outlands to give thanks that he did not live to see what became of his beloved planet. She believes that Andred's fall began due to Arkadian's deal with Torvald, and she thus intends to kill Arkadian and then join Andred in death. Meanwhile, Valyes is showing Arkadian around a hall of paintings; Arkadian is ostentatiously unimpressed, and Valyes, for the sake of the deal, hides his disgust at Arkadian's vulgarity. Arkadian then receives a phone call and returns to his ship; Leela follows him and overhears him receiving a warning about Matthias' intended betrayal. Instead of simply killing him where he stands, Leela threatens to torture him until he reveals the identity of his accomplice, but when she tries to attack him, his ship causes her knife to disintegrate in her hands. As he can't risk letting her tell the Time Lords what she's learned, Arkadian offers to buy her silence -- by restoring her sight. He does so temporarily, just long enough to prove to her that everybody can be bought if you know the price...
Annos and his guards have set up a containment field around the entrance to the catacombs in order to keep the zombies and pig-rats from getting out. Romana observes this and then asks Leela and K9 to accompany her on her mission, for old times' sake. However, K9 reveals that Matthias has offered him a position as the official pig-rat exterminator, and Romana must concede that this was a wise appointment. But she's even more shocked when Leela also turns down the invitation, claiming that she needs to keep Arkadian under guard -- and that she's grown old and weary of fighting. Romana can't believe that Leela has grown too scared to fight, but Leela insists that she's made her choice, and departs. The shaken Romana is left alone at last, abandoned by even her closest friends.
Morning dawns, and Arkadian visits Matthias and Narvin in the headquarters of the CIA. The temporal weapons have been loaded onto a battle-TARDIS, and once Romana and the reluctant Elbon are aboard, Arkadian hands his cell phone over to Narvin, telling him that a series of co-ordinates will be transferred to the TARDIS through the phone. The co-ordinates send the battle-TARDIS on a complex path through time and space that causes it to pass through Nekkistani, Monan, Sunari and even Dalek space; this is presumably to prevent it from being followed. However, Leela then arrives at the CIA and informs Narvin that Arkadian is working with a traitor; she knows him too well to trust his promises, and Arkadian now admits that the earlier light-show was a trick that affected her brain, not her optic nerves. The final set of co-ordinates sends the TARDIS accelerating out of range, and just as it disappears from the CIA's sensors, a surge from the cell phone shuts down all power in the Capitol. Arkadian flees into the darkened corridors, but Leela no longer needs light to track her prey...
Elbon screams in terror as the TARDIS accelerates, but instead of crashing, it materialises. Romana realises that the long flight was meant to give Arkadian or an associate time to de-list this TARDIS from the central registry, which means that Narvin will be unable to trace their location. She's already guessed where they are, and her suspicions are confirmed when she and Elbon emerge from the TARDIS to find themselves in an empty chamber with spaces on the walls where there used to be paintings. Indeed, although she and Elbon find themselves surrounded by Free Time's servitor androids, it's Irving Braxiatel who steps out to greet them. Romana concludes that his Collection has fallen on hard times and that he's engaged in arms dealing in order to fund its restoration, but he reveals that the truth is more complicated than that -- and the next stage of his plan involves the use of a Timescoop...
Leela pursues Arkadian into the biodata archives, and Narvin follows her in, telling her that there's only one exit; the Nekkistani and Monan have both put a bounty on Arkadian's head, and Narvin intends to collect it whether Arkadian is dead or alive. But at the last moment, K9 arrives and warns Leela not to kill Arkadian, and the shocked Leela realises that K9 is the one who's been supplying Arkadian with inside information. Instead of directly explaining himself, K9 contacts Braxiatel and informs him that all is ready -- and Braxiatel activates the Timescoop, removing the biodata archive and all its contents from Gallifrey. Back in the CIA headquarters, Henzil reports to Matthias that the power surge has shut down the force field around the catacombs, and Annos reports that it's also preventing them from sealing the entrances and exits from the Capitol. Soon, Free Time zombies are roaming the streets, Gallifrey is facing its most desperate crisis -- and President Matthias has no idea how to deal with the situation.
Leela and Narvin are surprised to find that Braxiatel has just stolen Gallifrey's entire biodata archive, and them along with it. Braxiatel admits that Pandora's weapons were a sideline; he did need to dispose of them, but his real goal was the archive all along, and he sold Arkadian his entire Collection in exchange for his help to get it. Braxiatel explains that in his time away from Gallifrey, he's heard rumours that his homeworld will soon be facing a terrible threat; ironically, it's something that the Imperiatrix would have been able to defeat, but that timeline is now defunct, and Gallifrey is too weak to fight what's coming. Braxiatel has thus chosen to salvage what he can from the ruins. The biodata archive contains the genetic sequences of every living Time Lord in all their regenerations, and Braxiatel has removed it to a secure location outside time and space; thus, once Gallifrey has fallen, he and his allies will be able to reconstruct it -- and its inhabitants.
Elbon demands the cure that Arkadian had promised, and Braxiatel presents the pig-rats that Gillestes used to develop the antidote -- but warns that there's a price for the cure. Since the virus remains dormant until the moment of regeneration, the only way to prevent it from being triggered is to remove the infected Time Lord's ability to regenerate. This was Free Time's plan all along -- not necessarily to destroy the Time Lords, but to deprive them of their advantage of near-immortality. Had the virus been released as Gillestes planned, the Time Lords would have been forced to eliminate their ability to regenerate to save their species. Braxiatel claims that Free Time is no longer a threat -- he's had his own adventures while in exile, and one day he may tell them -- but the virus has been released anyway. Braxiatel knew that Gallifrey was doomed and that the next President would go down with the planet, which is why he chose to appoint Matthias as his successor -- so that Romana would survive. Now she must choose the Time Lords' fate: either allow them to survive as mortals with a single life each, or allow them to die and replace them afterwards with a reconstruction from the biodata archive.
Before Romana can decide, Elbon grabs the pig-rats and runs for the battle-TARDIS, intending to release the cure himself. Too late, Romana realises why the mercenary medic returned to the society of the Time Lords that he'd once renounced; his medical station in the Outlands was infested with pig-rats, and at some point, Elbon must have been infected himself. His experiments were always meant to benefit himself. Unfortunately, Braxiatel programmed the servitor androids to guard the battle-TARDIS in order to prevent Arkadian from leaving with the temporal weapons, and when Elbon gets too close, one of the droids shoots and kills him, causing him to regenerate into a Free Time zombie. Arkadian pursues the zombie Elbon into the battle-TARDIS, intending to seize the temporal weapons and sell them to metal gentlemen of his acquaintance; however, he realises rather too late that jumping into a TARDIS with a Free Time zombie may not have been the safest move.
Ordinarily, the de-listed battle-TARDIS would be able to go anywhere, but when it dematerialises before Romana's eyes, she realises that traffic control back on Gallifrey must have been overrun by the zombies. The battle-TARDIS is no doubt on its way back to Gallifrey, carrying a consignment of booby-trapped temporal weapons and a cure that will rob the surviving Time Lords of the power of regeneration. Braxiatel admits that his plans have gone rather pear-shaped, and when Romana tries to use his Timescoop to pull the battle-TARDIS back out of the Vortex, the Timescoop burns out. Romana, K9, Leela, Braxiatel and Narvin are thus stuck outside normal space and time with no way to prevent the battle-TARDIS from reaching Gallifrey, and everyone turns to Romana for an answer.
"Right. What we're going to do is..."