On the planet Mendeb Three, scientists and lovers Kedin Ashar and Tevana Roslod, swept away by the enthusiasm of discovery, have agreed to supply Duke Vethran of Gonfallon with weapons based on their new technologies in exchange for lands and funding. But they and their friend Madok eventually start to worry about the Duke's ambitions; are they creating a monster they will be unable to escape themselves? Meanwhile, the TARDIS materialises in a room full of electronic equipment on the oppressively warm Mendeb Two. The Doctor suspects that his ship has brought him here for a reason, but is unable to determine what that reason is and thus decides to go someplace cooler. Before leaving, he tells Jamie to pick up a souvenir, to remind him to return one day...

Much later in the Doctor's lifetime, Ace finds the "souvenir" in a forgotten storeroom on the TARDIS, finally reminding the Doctor of his long-overdue appointement. He now knows that there are two human colonies in the Mendeb system, both abandoned centuries ago when the TAM corporation pulled out and took its copyrighted technology with it. According to Matrix projections of the future, the colonies should have rediscovered space travel by now, and the Moonstar, the space station left in orbit between planets Two and Three, should be a trading port. The cooler climate and extensive resources of Mendeb Three will probably have led to a technological imbalance, offset only by the fact that the colonists of Two retained a communications system as a link between the northern and southern hemispheres. At least, they did until the Second Doctor "borrowed" it...

The Doctor must take responsibility for his actions and ensure that the two worlds re-establish contact peacefully. Ace, assuring the Doctor that she can look after herself, offers to visit the space station while the Doctor returns the PCS to Mendeb Two. The Doctor therefore drops Ace in a deserted part of the station and continues on to Mendeb Two... only to materialise in the ruins of a once peaceful village. The sole remaining villager, Bep-Wor, tells the Doctor that soon after contact was lost with the southern hemisphere, mysterious invaders began to kidnap the people of Two and burn them out of their homes. Furious with himself, the Doctor sets off to put things right. He is accompanied by Bep-Wor, who is desperate to find out what has happened to his missing wife Kia-Ga.

The station is all but deserted, and while exploring, Ace finds six scruffy, dangerous-looking men attacking a man in an elaborate uniform. She helps hold off the attackers until reinforcements arrive, and the man she saved, Kedin, is impressed by her combat skills, brightness and intelligence, and flirts with her to find out what she knows about the station. Believing that their attraction is mutual, Ace eventually accepts his claim that his attackers were mutineers, and sleeps with him, promising to show him how to operate the satellite's still dormant systems. While alone, she discovers that Kedin's cabin is the station's auxiliary control room, and reactivates its communications console -- only to see, on the surveillance monitors, a cargo hold containing thousands of terrified human beings. Furious, she confronts Kedin, who admits that he is selling the natives of Mendeb Two as slaves. He insists that this is a temporary measure, to fund a secret uprising against the tyrant who rules his homeworld, but Ace doesn't believe his claims and vows to stop him. Madok surprises and knocks her out, but it is clear that she knows too much, and that she can turn the satellite itself against them if she so desires. Kedin and Madok decide that they have no choice but to process her along with the other slaves. The best they can do for her is dose her with an untested chemical which they believe will replicate the effects of the drug SS10 but wear off eventually... they hope.

The Doctor and Bep-Wor find humans from Mendeb Three marching captives out of their homes and burning the villages behind them so the villagers have nowhere to return to. The Doctor allows himself to be captured, and he and his fellow slaves are taken to the Moonstar in a crowded, poorly ventilated and unheated cargo shuttle. The Doctor sees the prisoners through their ordeal, and when he uses CPR to revive a dead man, Bep-Wor becomes convinced that the Doctor is the man who can save them all. The prisoners are left without food for several hours, and then provided with soup; however, the Doctor tastes the soup first and realises that it has been drugged. He and Bep-Wor stop as many people as they can from drinking the soup, and the Doctor provides them with a substitute from a seemingly bottomless flask with a dimensional link to the TARDIS food machine. Those who did drink the soup lose all conscious volition, and obey their captors' commands without question. The Doctor urges the others to play along and wait their chance. However, when they arrive on Mendeb Three, the commissioner in charge of accepting the consignment orders an elderly woman to chop off her own hand as a test, and the Doctor intervenes, thus proving that the chemical doesn't affect him. Bep-Wor and the other slaves begin to chant the Doctor's name in unison, and the unnerved commissioner refuses to pay for this "faulty shipment" and has the slaves taken away for examination.

Madok returns to Mendeb Three to ensure that all is ready for the uprising. Thanks to Ace, Kedin is now able to relay signals from his fortress through the Moonstar, thus co-ordinating his army across Gonfallon. Madok is sent to rescue Tevana, whom Vethran has been holding hostage to ensure Kedin's co-operation; however, he first makes a detour to ensure that Ace is being treated well. She has been purchased by prominent citizen Balon Ferud, and is being trained by his chamberlain Tragar; already, her unique attitude, clothing and manner of speech have attracted a great deal of attention, as has her ability to defend herself against an attacker twice her size. It is too dangerous for Madok to attempt a rescue, and he thus continues on to Tevana's castle -- only to find that the delay has cost him his chance to free her. The strange behaviour of the latest shipment of Twos has aroused Vethran's suspicions, and he has pushed through a new law which makes it illegal for unmarried women to own land. Tevana's lands now belong to Vethran, and she is to be brought closer to Gonfallon for her "protection". Madok has no choice but to report his failure to Kedin, who can only hope that the fact that Tevana remains a hostage will lure Vethran into a false sense of security. The diversion they had planned to divide Vethran's forces onto two fronts will now have to serve as Tevana's rescue as well.

The Doctor, Bep-Wor and their fellow slaves are taken to a nearby farm to await examination, but when Bep-Wor learns from one of the farm's slaves that Kia-Ga was recently sold on from this very farm, he becomes determined to break out and find her. The Doctor would prefer to continue the charade until he can get to someone in authority, but he concedes that it will be difficult if not impossible for the slaves to escape once they have been taken to the city, and agrees to help them. The guards, believing the Twos to be docile, are easily surprised and overpowered, but although the Doctor insists that they simply be tied up, Bep-Wor and his fellow Twos in fact kill them and torture the farmer to learn which farm purchased Kia-Ga. The slaves march to that farm, where the Doctor tries to speak with its owner. However, the farmer is confused and frightened by the crowd of hostile Twos, and strikes the Doctor down. Upon seeing this, the mob descends upon the farm in a frenzy, killing the farmer and his family before the Doctor can stop them.

Bep-Wor is reunited with Kia-Ga, only to find that, like all other slaves, she has been given the drug SS10. Although she retains her memories and basic personality traits, she has no will of her own, and even the Doctor is not sure if she will ever recover. The army of free Twos approaches Gonfallon City, and on the way, there are further skirmishes with Threes and their slaves; some are bloodless, and some, to the Doctor's despair, are not. Whenever they can, the Twos free their fellow slaves, and Bep-Wor tells the drugged Twos that the Doctor is their new master in order to keep them united. Bep-Wor himself is respected due to his closeness to the Doctor, and is regarded by the Twos as their general; however, privately he knows that despite their small victories against local forces, they will be no match for the full military might of Gonfallon City.

As the Twos approach the city, they see a fleet of ships landing nearby, and the Doctor and Bep-Wor investigate to find Kedin Ashar preparing to launch his attack. Kedin recognises the Doctor from Ace's descriptions, and explains that he is simply trying to correct the mistake he made in helping the ruthless Vethran to the throne. He thought he was the Duke's only scientist, but there were others, and one of them learned how to synthesise the drug SS10 from a harmless narcotic plant. When Vethran took Kedin's lover Tevana hostage, Kedin was forced to lead the war against Two to appease Vethran's ambitions. He intends, however, to overthrow Vethran and put an end to the slave trade, and he asks the Doctor and Bep-Wor to support him. The Doctor and Bep-Wor, considering what they have learned, return to their army only to find that in their absence the others have been recaptured by a patrol from the city. The Twos are thrown into the palace dungeons, where Vethran, rather than interrogate the Doctor, simply forces him to drink a fatal poison and chains up his body in Traitor's Way.

Believing that the rumours of mysterious movement in the forest have now been explained, Vethran orders his soldiers to stand down and invites his loyal courtiers to a feast. Balon Ferud attends with his strange slave Ace, who finds her volition returning to her as she serves the courtiers. Furious about what has been done to her, she goes off looking for damage to do, and as there is no known cure for the effects of SS10, everyone who sees her assumes that she is obeying her master's orders and thus does not question her presence. While exploring, Ace finds the lab where SS10 is manufactured, and learns that it was not Kedin who was responsible for its creation. She also finds soldiers bringing food to the captive Tevana, and frees Bep-Wor and his fellow Twos from the dungeons.

Since Vethran's patrols have returned, believing the emergency over, Kedin is unopposed when he leads his rebel army into the city -- unaware until too late that Tevana is being held within Vethran's palace itself. Ace sees the rebels attacking Vethran's palace and plants explosives on the outer wall, bringing it down and letting them in. Kedin's soldiers fight their way to the throne room, where Bep-Wor's army bursts in, surprising Vethran's men and taking them down from behind. Vethran has Tevana brought to him as a hostage, intending to stall Kedin with negotiations until reinforcements arrive. He also slips Ferud a vial of SS10, telling him to get close to Kedin and throw it in his face. They remain unaware that Ace's free will has returned, however, and she manages to slip a sample of SS10 from the laboratory into Vethran's drink. As soon as he drinks, she shouts out a warning to Kedin, and Ferud is arrested while Vethran falls into a drugged stupor. It appears that Kedin has won -- until he realises that Tevana is not responding to his arrival, and Ace realises that the food the soldiers brought to her was drugged. Unable to do anything for the shattered Kedin, Ace has the Doctor's body cut down from Traitor's Way, guessing correctly that he has placed himself in a healing coma and will soon revive.

The battle has been won, but at a cost. When the Doctor analyses SS10 he discovers that the drug cauterises the parts of the brain responsible for free will, and that the resulting brain damage is irreversible. When Bep-Wor learns this, he shoots both Kia-Ga and himself. Kedin will now set about the difficult task of restoring proper rule to his planet and making war reparations to Two, but he will have to do it without Tevana. Ace, who has forgiven him his earlier actions, wants to stay and help him, but the Doctor -- who still blames himself for the war and takes his inability to save the victims of SS10 personally -- doesn't seem to acknowledge her wishes. Kedin advises Ace to leave with the Doctor, knowing that her place is with him. If she doesn't get in the TARDIS she'll regret it; maybe not today, maybe not tomorrow, but soon and for the rest of her life. She accepts this, and departs with the Doctor, leaving the people of Mendeb Two and Three to build a new future in which they are free.