A medical supply spaceship unexpectedly comes under attack from an unknown enemy, and the Doctor and Mel are trapped aboard. The Doctor catches a glimpse of the attacker through a porthole, and finds it oddly familiar; however, the medical ship’s reactor core has been breached, and he doesn’t have time to identify the enemy ship. Instead, he bundles Mel into a nearby escape pod, ensuring her safety before he goes hunting for the TARDIS. It’s in the ship’s engine room, but just as the Doctor boards, the ship’s reactor finally overloads and explodes. Mel’s escape pod is just about to clear the blast zone when the ship explodes, and the pod’s navigation systems adjust course accordingly to take Mel to the nearest inhabitable planet.

That planet is Lethe, a domed mining colony where water is rationed and the colonists have subcutaneous implants to monitor their movement and well-being. Mel is welcomed into the colony, and as weeks pass with no sign of the Doctor, her programming expertise lands her a position in the science labs under the avuncular, wheelchair-bound Professor Vaso. Vaso and his team, Sonali and Geoff, are working to upgrade a number of ancient service robots recently unearthed by the colony’s mining engineers; Mel helps them to upgrade the software, and enjoys a mild flirtation with Geoff, who would clearly like for her to be more than just a friend. Over two months pass, and eventually, their work attracts the attention of the Outreach corporation, which sends a party of key executives sets off for Lethe to witness a demonstration.

The Doctor awakens to find that he’s been restrained in a large chamber aboard an interstellar spaceship -- a prisoner of the Daleks. He resigns himself to torture and interrogation, but to his surprise, the Black Dalek reveals that they need his help. The Daleks timescooped the Doctor and his TARDIS away from the medical ship seconds before its destruction because they’re facing a threat that they can’t deal with themselves; the world on which the threat is being created apparently contains an airborne toxin that is harmless to humans but lethal to Daleks...

On Lethe, Mel has finished reconfiguring the robots’ multitasking procedures. Geoff makes a point of complimenting her on her work, and Mel obviously appreciates the flattery. Vaso supervises as the team prepares to run their “Juggernaut” through its paces, and once activated, it speaks in a bubbling, electronic voice -- which nobody present has any way of knowing is the voice of a Mechonoid. The Juggernaut accepts English input, and proves capable of performing both simple and complex mechanical tasks. Word arrives that the shuttle Atalanta has entered the solar system, and Vaso orders Geoff and Sonali to prepare for the Outreach executives’ arrival while he chats privately with Mel. Vaso is the sole survivor of a terrible shuttle crash that took the lives of several colonists and damaged a sector of the colony beyond repair; however, he feels that he has made partial amends through the Juggernaut programme, and as Mel has been such a vital part of that programme, he invites her to take a permanent position on his staff. Mel is tempted, but admits that she’s still waiting to hear from the Doctor -- and though Vaso reacts oddly when Mel mentions the Doctor’s name, he covers his reaction and assures her that his offer still remains open should she change her mind.

Geoff then contacts Vaso to report that he’s spotted sensor ghosts near the damaged sector; the motion sensors are still in a state of disrepair, and sometimes seem to detect movement where there is none. Vaso authorises him to give the system a once-over, but while doing so, Geoff and Sonali spot a strange shadow on one of the surveillance monitors. It doesn’t look like a human, and none of the mining robots should be in that part of the colony. Disturbed, Geoff contacts security officer Loewen and asks her to check out the area -- but advises her to take a staser, just in case there is something down there.

The Daleks explain that the ship that was taking Davros to trial on Skaro was attacked and shot down. The Daleks believed that Davros had been killed, but recently they received reports indicating that he had infiltrated the colony on Lethe. The Daleks promise to let the Doctor and Mel leave freely once they’ve found out what Davros is up to, and the Doctor reluctantly promises to help them for Mel’s sake. The Daleks transmat him into the subterranean caverns beneath the colony, informing him that they will be observing him via nanocams they have placed throughout the colony. Of course, the Doctor doesn’t trust them an inch -- and indeed, they have their own plans for him once his mission is complete.

The Outreach executives arrive on Lethe, and their implant chips are scanned and updated before they attend the others in the lab. Sonali, Geoff and Mel are nervous, but “Vaso” is confident that the corporation understands and appreciates the work they’ve done; they simply wish to see the Juggernauts for themselves before committing to the project. The chief executive, Mr Brauer, then enters the lab, followed by his associates, Valmont, Ferris, and Kryson. They have never actually seen Vaso in person, as he claims to be camera-shy due to the injuries he suffered in the shuttle crash. Kryson seems startled when he is introduced to Vaso, but he covers his reaction, claiming that he’s been ill; Brauer explains that Kryson suffers from space sickness and spent most of the journey in his quarters, taking medicine provided by his doctor. Vaso and his team now introduce the executives to the Juggernauts, and the demonstration goes extremely well. Brauer decides to rest for a while before deciding what to do, and in passing, he comments on how much clout Vaso has. Commander Eckhardt is in charge of mining and production, while Vaso is only in charge of the colony’s scientific division; yet Vaso is now so respected, it’s almost as if he runs the whole colony himself.

Sonali shows Brauer and the executives to the colony’s guest quarters, while Geoff and Mel visit the canteen for supper. There, they chat about their pasts and their intentions for the future. Geoff hasn’t been back to Earth for a long time; his parents died in the Kensington disaster of ’97, and his only living relative is a cousin in Australia with whom he’s lost touch. Mel admits that she too has been away from Earth for some time, and that the flat interior of the TARDIS is beginning to bore her. She impulsively kisses Geoff, who admits that part of him hopes the Doctor never turns up to take her away. Mel decides to return to her quarters -- alone -- but before she goes, Geoff gives her a gift to remember him by if and when she does leave: an antique music box that plays Ave Maria.

Loewen has checked out the motion sensors by the damaged sector, but has found nothing wrong with them. She reports in to maintenance and prepares to return to her quarters -- but then stumbles across something she really shouldn’t have seen. Soon she is dead, and Davros, realising that she’ll be missed, nevertheless orders certain of his associates to begin carving up her body for later use. When Loewen fails to report in, security starts a sweep around the damaged sector, and the duty commander reports to Geoff. He is disturbed by the news, but has no idea what’s really happened to Loewen...

The Doctor finds his way out of the mines and eventually locates Mel’s quarters. Delighted, Mel tells him about the work she’s been doing, but in turn, the Doctor has to break the bad news that friendly Professor Vaso is in fact one of the most evil men in the galaxy. Mel can’t accept this, particularly as she perceives Vaso not as the Doctor does, but as a handsome old man in an ordinary wheelchair. The Doctor understands that it’s a lot for her to take in, and promises to let her catch up on her sleep while he investigates on his own; despite their disagreement, however, they are happy to see each other. The Doctor leaves Mel to rest while he explores the colony, and eventually, as dawn breaks, he finds his way to the damaged sector. The colony computer informs him that this sector was used for storage, surgery and emergency environmental systems, all of which were relocated after the crash 716 days ago. However, the door to the supposedly abandoned sector then opens, and the Doctor hides and listens as Davros emerges, giving instructions to someone -- or something.

As morning breaks, Mel and her friends assemble in the laboratory to hear what Brauer has to say. He informs them that his superiors are very impressed with the work that has been done here... but they now intend to take the project into their own hands and have their own, hand-picked scientists and technicians develop the Juggernauts further. Brauer thus orders Vaso and his team to suspend their work temporarily, and refuses to negotiate; if they refuse to accept this ultimatum, then their work will be confiscated, their contracts with Outreach will be terminated, and the project will be taken out of their hands permanently. Brauer gives Vaso until tomorrow morning to decide, and departs, leaving Vaso and his team stunned by this development.

Vaso leaves, claiming that he wants to be on his own, while the frustrated Mel, Sonali and Geoff retire to the canteen to drown their sorrows. But while Brauer is taking some personal quiet time, Vaso invites Kryson to meet privately with him on Observation Deck 7. There, he reveals that he knows Kryson knows the truth about him, and Kryson admits that he recognised him as Davros at once. Davros has been using an engineered virus to alter the colonists’ perceptions -- but Kryson’s story about space sickness was a cover for the fact that he’s a drug addict, his bloodstream thick with chemical stimulants that have countered the effect of Davros’ virus. Davros now threatens to release chemicals into the atmosphere that will target and destroy Kryson’s scarred brain tissue, unless Kryson uses his influence to ensure that the Juggernaut programme remains in the hands of Davros’ team. Davros will deal with Brauer by other means -- and he now summons those means to the observation deck to receive orders.

On closer inspection, the Daleks prove to be badly damaged white Daleks, from Nekros; Davros was not the sole survivor of the crash after all. However, Davros did not bring them here to deal with the Doctor, and he orders them to remain in the observation deck until he has need of them. Davros dismisses Kryson, warning him to tell no one of their conversation, while he shows the Doctor what he and his colleagues -- including Mel -- have created. Kryson retreats to his quarters to take another dose of stimulants, but Brauer bursts in on him, revealing that he’s bribed the colony security guards and knows that Kryson was meeting secretly with “Vaso”. When he threatens to have Kryson’s entire portfolio liquidated, Kryson admits that Vaso is blackmailing him into finding a way to prevent the suspension of the Juggernaut programme. Furious, Brauer sets off to confront Vaso in person.

The Doctor is expecting to find that Davros has been designing a new wave of Daleks, and is subsequently surprised to find himself facing a group of modified Mechonoids. Before Davros can demonstrate them, however, Brauer storms into the lab and announces that Vaso’s involvement with the Juggernauts is now at an end. Davros therefore summons his Daleks to the laboratory and deactivates Brauer’s implant, allowing him to see Davros as he really is. Brauer promptly pulls a gun on Davros, intending to turn him in for the reward, and before the Doctor can intervene, the Daleks respond to this threat and gun Brauer down where he stands. Davros orders a Dalek to escort the terrified Kryson back to his quarters, and then contacts colony security and requests that all outbound communications be jammed until further notice. The Doctor is furious, but with the Daleks in the room, he has little choice but to listen as Davros explains the true purpose of the Juggernaut programme.

Geoff, Sonali and Mel are drowning their sorrows in the bar, wondering what Vaso’s response to the ultimatum will be and passing the time with a game of slitherball. Mel admits that the Doctor has returned, and Geoff tries not to show his disappointment. Mel is then called to the lab, and she bids goodbye to her friends and responds. Meanwhile, on the Black Dalek’s spaceship, the grey Daleks continue to monitor the situation on Lethe. They are now aware that Daleks loyal to Davros are present and have fired weapons within the colony; however, they continue waiting for the Doctor to complete his mission before they move in.

Mel arrives in the laboratory, but to her horror, she sees Brauer’s body lying on the floor -- and Davros sheds his disguise and reveals himself as he truly is. He explains that he had to hide away to avoid those who consider his past sins unforgivable, but insists that everything he’s done as Professor Vaso has been for the greater good; with the others’ unwitting help, he has transformed the Mechonoids into the ultimate Dalek killers. With Kryson’s assistance, Outreach will soon put the Juggernauts into mass production, creating a self-sufficient, self-repairing, and, eventually, self-replicating army with which to destroy the Daleks -- something, Davros points out, that the Doctor once failed to do himself. The Doctor insists that this is because he considers all the past and future repercussions of his actions, but Davros suspects that the Doctor in fact knows the Daleks’ ultimate fate already -- and may have had a part in it. In any case, he assures the Doctor that he has no intention of replacing one threat to the galaxy with another; once the Daleks have been wiped out, the Juggernauts will revert to their default Mechonoid programming, and serve the human race as terraformers and service robots.

Davros requests the Doctor’s help, but the Doctor reminds him that they’ve failed to work together before. Nevertheless, Davros orders one of the Juggernauts to escort him and Mel back to Mel’s quarters so they can consider his offer. He then summons Kryson back to the laboratory to discuss how to deal with Brauer’s unfortunate “accident”. The surveillance monitors in the guest quarters indicate that the other executives don’t trust Kryson, and in any case, he’s very low down in the chain of command. To Kryson’s horror, Davros therefore sends a Dalek into the guest quarters, and ensure that the other executives meet with a similarly unfortunate “accident”...

On their way back to Mel’s quarters, Mel reveals that she’s programmed a backdoor command into the Juggernaut software, giving her complete control of the Juggernauts when she recites her home address in Pease Pottage. She does so now, shutting down their escort -- but when she and the Doctor examine it more closely, they discover that human blood is leaking from its central hub. When the Doctor opens up the hub, he and Mel discover that Davros has modified the Juggernaut using human nervous tissue; the Juggernauts are no longer robots, but cyborgs created with human body parts. Sickened, Mel allows the Doctor to close up the central hub and reactivates the Juggernaut to avoid suspicion.

Sonali wonders why Mel was summoned to the laboratory by herself, and when she and Geoff try to find out, they discover that Vaso has shut down certain monitoring stations: the lab, the guest quarters, the shuttle bay, and the abandoned surgery in the damaged sector. Geoff bypasses the security overrides, and to his and Sonali’s horror, they see that a Dalek has slaughtered the Outreach executives and that Loewen’s decapitated body is lying in the abandoned surgery. Meanwhile, in the laboratory, Davros activates a new Juggernaut, which refers to itself as Loewen before Davros activates its personality print override, erasing all trace of Loewen’s personality. He now reveals the truth about the Juggernauts to the appalled Kryson, but assures him that there’s no need to kill people in order to build the Juggernauts. Earth has passed laws regarding mandatory organ donation; Kryson merely needs to negotiate contracts with the hospitals to ensure that they ship vital organs to Outreach when their patients pass away from natural causes. Despite himself, Kryson finds that he is considering the suggestion.

Back in her quarters, Mel accesses the colony’s medical records on the Doctor’s instructions, and discovers a discrepancy involving the deaths of 12 miners in a cave-in four months after Davros arrived on Lethe. At least one of the victims mysteriously lost 470 grams of body mass between his death and his post-mortem, and that’s just over the average size of the human heart. Mel points out that this occurred three months before the Mechonoids were unearthed, but the Doctor suspects that Davros initially intended to continue the experiments he’d begun on Nekros with the intention of turning humans into Daleks, before he became diverted by the possibilities of the Juggernauts. Mel sets about erasing all data on the Juggernaut programme from the Lethe mainframe, but it occurs to her that she’s only ever seen three Juggernauts -- so what happened to the other nine victims of the cave-in?

Geoff then contacts Mel to warn her what he’s seen on the monitors, and the Doctor advises him and Sonali to lay low until the danger has passed. However, they are unwilling to stand by while Daleks invade the colony, and they thus contact their fellow colonists to warn them of the danger. The colonists agree that the best course of action is to evacuate in the Atalanta; unfortunately, when they arrive in the shuttle bay, they find that two of Davros’ Daleks are standing guard between the entrance and the executives’ shuttle.

Mel finishes her work and shuts down her Juggernaut escort, and she and the Doctor return to the laboratory to deal with Davros. He gives Davros one last chance to shut down his work, but Davros refuses; Kryson has come around, and Mel’s work has only delayed matters slightly, as most of the schematics for the Juggernauts have been sent on ahead to the Outreach corporation on Earth. The Doctor thus has no choice but to call in reinforcements -- and the grey Daleks, who have been monitoring his progress, now move into the colony, destroying the white Daleks when they refuse to change their loyalties. Mel is appalled and Davros is very nearly amused to realise that the Doctor has been working with the Daleks all along without their knowledge; nevertheless, Davros refuses to surrender meekly, and orders the Juggernauts to engage defensive mode. Kryson steps in, refusing to co-operate with Davros unless he allows the Doctor to live. However, Davros reveals that he’s stored the schematics for the Juggernaut cybernetic enhancements in a separate system; if he is killed now or turned over to the Daleks for trial, then Outreach will be unable to build Juggernauts to his specifications.

The Juggernauts’ approach is blocked by a force field, apparently a backup in case the outer doors failed. With Mel’s help, the Doctor locates an access panel and deactivates the force field, and once the Juggernauts have trundled past, he and Mel pop through the door to investigate what’s really been going on in the damaged sector. Davros’ tracks in the dust and the hum of machinery lead them to an assembly line where Juggernauts are making more of themselves; as Davros had claimed, they are self-replicating with the right resources. Fortunately, these Juggernauts are programmed to focus exclusively on manufacturing, and the Doctor and Mel are thus able to sabotage the assembly line without being noticed. As the Juggernauts set about repairing the damage, however, security-class Juggernauts arrive to deal with the threat, and the Doctor and Mel are forced to run for it. Their flight takes them through the abandoned surgery, where they find the remains of Loewen; the Doctor studies her body and determines that she must have been killed by a Dalek, presumably after stumbling across Davros’ operations -- and that Davros subsequently harvested her organs to create another Juggernaut.

The grey Daleks have destroyed the Juggernauts in the laboratory and taken Davros prisoner. He claims to have been working for their benefit, as the modifications he developed on the Juggernauts can be adapted to improve the Daleks themselves; however, they don’t believe him, and Kryson refuses to support his claims. Kryson can now walk again, but as he tries to storm out of the laboratory in disgust, he finds his way blocked by the Daleks. Meanwhile, more of Davros’ Daleks continue to block the colonists’ way into the Atalanta, and Geoff thus bursts out of hiding and lures them away so his friends can get aboard. The colonists board the shuttle safely, but Geoff then finds that he is unable to shake off his pursuers. Unwilling to lead them back to the Atalanta, Geoff realises that he has no choice but to lure them into an airlock -- and despite Sonali’s protests, Geoff seals the inner door behind himself and the Daleks and opens the outer door, exposing the Daleks -- and himself -- to the lethal, 200-mile-an-hour methane winds outside the colony.

The Doctor and Mel return to the laboratory, where the Doctor informs the Daleks that he’s carried out his end of the bargain and destroyed the Juggernaut production line. However, the Daleks now reveal that they were responsible for the attack on the medical ship, and that they guided Mel’s escape pod to Lethe, engineering this entire situation in order to trick the Doctor into helping them defeat Davros. Now that he has done so, they intend to take him back to Skaro to learn the secrets of the TARDIS. Davros speaks up on Mel’s behalf, claiming that she could be of use to the Daleks, but the Daleks ignore him and prepare to exterminate her and Kryson. Before they can do so, however, Juggernaut reinforcements arrive and attack the Daleks, forcing them to retreat.

Davros now has the upper hand, and he thus orders the Juggernauts to punish Kryson for his betrayal. Before Mel can react, the Juggernauts move forward and crush Kryson to death between themselves. Sonali’s voice then comes over the PA, advising all remaining colonists to retreat to the shuttle bay and evacuate. Davros prepares to order the Juggernauts into action to prevent the colonists from escaping -- but Mel has had enough, and before the Doctor realises what she’s doing, she uses her backdoor command to take control of the Juggernauts and orders them to consider Davros a threat. She then leaves the laboratory, and the Doctor, though appalled, has little choice but to follow her and leave the terrified Davros to his fate. Meanwhile, the grey Daleks and the Juggernauts have engaged in battle throughout the colony, and, realising that they’re outnumbered, the grey Daleks call back to their ship for reinforcements.

Mel refuses to discuss what she’s done, and the Doctor, shaken, helps her to find an intercom so she can contact her friends. She gets through to Sonali, but is horrified to learn that Geoff is dead. The Doctor warns Sonali to leave immediately before more Daleks arrive, and she does so, wishing the Doctor and Mel good luck. Mel then demands to know what Davros meant when he claimed the Doctor once had the chance to wipe out the Daleks but did nothing. The Doctor can only explain that changing the course of history can have devastating consequences that even the Time Lords can’t fully understand; but this is small comfort to Mel, who knows that Geoff was becoming more than just a friend to her.

As the Doctor and Mel head for the transmat, they run into Davros -- or what’s left of him. The Juggernaut attack has left his flesh seared and his body leaking blood, and he can still feel the injuries though his chair is pumping his body full of painkillers. He warns the Doctor and Mel that the attack has triggered his chair’s self-destruct mechanism, but it’s damaged, and there’s no telling when it will go off; he thus urges them to flee while they still can. The Doctor and Mel sadly take their leave and return to the transmat dais, where they see more Daleks arriving from the ship; once the coast is clear, they board the dais and return to the ship, intending to surrender immediately if there are Daleks in the transmat chamber when they arrive. Meanwhile, the Dalek reinforcements catch up with Davros, who admits that he’s impressed with the Daleks’ ability to destroy his Juggernauts. But it’s too late for them now in any case, as Davros’ self-destruct mechanism finally detonates, destroying the colony and taking the Daleks with it.