Two humans, Hoyer and Fantham, manage to evade the Cybermen searching for them and reach their destination, the Chronosphere. The Doctor is already locked into its matrix, and they send him from 1951 to a nexus point in the year 3286. If all goes well, the Doctor will change the web of Time, and Hoyer and Fantham will cease to exist.

A human survey team lands on a deserted planet to find out what happened to two other, missing survey teams. Exactly one day after the previous disappearance, Osborn contacts the mothership to report that his team has found nothing -- but then a wave of temporal energy washes out of the structure which Osborn believes to be an ancient temple. As the signal begins to break up, the desperate Osborn warns his contact, Krueger, that there’s a Cyberman at the heart of the temporal wave...

The mention of Cybermen naturally causes concern, and soon another expedition has arrived on the planet, accompanied by the Doctor and Evelyn. Administrator David Isherwood isn’t pleased to have been saddled with strangers, and he turns Evelyn over to another man he’s been stuck with -- Doctor Reece Goddard, an expert on Cybermen who seems awed to learn that Evelyn is a companion of the legendary Doctor. Evelyn modestly dismisses her own exploits and inquires about the Cybermen, and Dr. Goddard gives her a potted history of the race, from their origins on Mondas through to their colonisation of other worlds, the destruction of Mondas, and the Orion wars. The Cybermen have learned from each defeat, and have constantly adapted their design to overcome their early weaknesses, such as radiation and gold dust. However, they haven’t been heard from in centuries, which is why Central became so worried when Osborn went missing after he reported seeing a Cyberman...

Inside the “temple”, the Doctor is studying the hieroglyphs on the walls while Renchard and Carey, unable to find any sign of the missing expeditions, amuse themselves by generating an echo field to block the transmissions from their subcutaneous transponders. The Doctor points out certain architectural oddities which suggest that this building was meant to be easier to get into than out of, and a large stone doorway which is much thinner than the others. Scans indicate a solid stone wall on the other side, which suggests that this stone is not a door but a cover. Savage sends Renchard back to fetch vacuum cylinders, with which to preserve whatever lies behind the covering, and she, Carey and the Doctor attempt to move it aside. However, the Doctor then notices scratches which suggest that the cover has been moved before; perhaps this is what unleashed the temporal wave in the first place. Savage’s professionalism slips, as she believes her missing friends and colleagues may be trapped behind the cover, and she feels the Doctor is risking their lives with unnecessary caution. As they argue, however, the covering vanishes to be replaced by a translucent membrane, behind which they can see a room too large to fit into the small space behind the covering. The Doctor realizes the truth, but Savage again ignores his pleas for caution and sticks her hand through the membrane -- and is yanked through, screaming, by something on the other side.

Evelyn doesn’t understand Isherwood’s mention of “transponders,” and Goddard explains that the expedition members have tiny transmitters implanted in their skin -- apart from the Doctor and Evelyn, and Goddard himself, who claims to be allergic. Savage’s transponder signal returns, but Evelyn remains concerned -- and her concerns are justified when the Doctor and Carey return with the Cyberman that used to be Savage in close pursuit. The “temple” is a time gate, and Savage’s conversion, which should have taken months, has taken place in subjective moments. Evelyn inadvertently gives away the Doctor’s identity, and Savage orders him to hand over his TARDIS on pain of watching his four friends die. Puzzled, the Doctor lets this slide for the moment but questions why Savage’s Controller hasn’t passed through the portal itself. Perhaps it’s unable to survive the journey, which is why it needs the TARDIS. The Doctor doesn’t yet realize that the Controller has been listening to this conversation, as Savage’s transponder has been reconfigured to transmit and receive through the portal...

Following the Controller’s orders, Savage separates the Doctor from the others and threatens to kill them slowly unless he surrenders the TARDIS. He refuses to do so, knowing that Cybermen with unlimited time travel would pose a far greater threat to the Universe. Savage gives the Doctor a few minutes to decide, and he, Evelyn and Goddard discuss their time limit -- and the fact that the temporal wave will shortly wash out from the portal, presumably transporting them all into the Cyber Controller’s domain in any case. The Doctor is convinced that the portal is the creation of another alien race, and that the Cyber Controller doesn’t know how to use it properly. Perhaps the Doctor can take advantage of that fact by giving the Cybermen incorrect operating instructions. But something which Savage had said earlier is nagging at him...

Isherwood makes a deal with Savage, offering to use the expedition’s sealant packs to create a mould of the TARDIS lock in exchange for their lives. Savage accepts his terms and orders her troops to take the TARDIS into the time portal, intending to betray Isherwood and take him through as well. However, when the Cybermen attempt to carry the TARDIS through the temple door they find it won’t fit through -- something they really should have noticed earlier. The Doctor, watching them, concludes that there’s something seriously wrong with these Cybermen, and he and Goddard set off to confront Savage while Evelyn keeps Isherwood occupied.

The Doctor taunts Savage and notes that her cybernetic parts are falling off -- this is not just decay, it’s the result of poor workmanship. Savage explains that the Controller exists in the distant future, at a time when the Cybermen are all but extinct; only a handful survived the wars, and they fled to a water world where they found this time portal. All attempts to travel back through Time failed, as the troopers’ cybernetic implants began to disintegrate on the other side; this is why they need the TARDIS. The Doctor theorizes that the water world of the future and this desert planet of the present are the same planet, and that its inhabitants built the portal to travel to a time when their world was habitable again -- only to be wiped out by the Cybermen. He also deduces that Savage is in contact with the Controller, which means that if he can sever their link the Cybermen on this side would be helpless.

The Doctor sets off to confront Isherwood, and informs him that Savage can listen in on all of their conversations through their transponder. Upon hearing this, Renchard reactivates the echo field which he and Carey had created earlier as a joke, thus shielding their conversation. The Doctor needs someone to dismantle whatever the Cybermen are using as a relay through the portal, and Isherwood suggests sending Evelyn and Goddard, as neither has a transponder and thus they cannot be detected by the Cybermen. Unfortunately, Goddard has taken the initiative and taken Evelyn and Carey into the ruins to dismantle the relay -- and as Carey does still have a transponder, the Cybermen are aware of their presence. The Doctor heads to the rescue, taking Renchard in the hope that his echo field will prevent the Cybermen from detecting them, and advises Isherwood to go through Goddard’s belongings while they’re gone. He’s beginning to suspect that Goddard knows more than he’s saying...

Carey is placed in the conversion chamber by a Cyberman he recognizes as Richie Allen, a former friend from one of the previous expeditions. But his pleas for mercy are ignored, and the conversion machinery cuts into his flesh, replacing his organic parts with bionic implants and reprogramming his brain. Soon Carey is himself a Cyberman.

Goddard informs the Doctor and Renchard of Evelyn and Carey’s fate, and Savage then confronts the Doctor, once again demanding the TARDIS and this time using Evelyn as a bargaining chip. Infuriated to learn that Carey’s conversion has already begun, the Doctor tries to reach out to the human part of Savage, but fails. When Savage threatens to crush Renchard’s arm before his eyes, the Doctor reluctantly leads her to the TARDIS -- but she slips up when she rushes him, claiming that there isn’t time to enlarge the opening to the temple. The Doctor realizes that the Cybermen aren’t in control of the temporal wave after all, which means that he just has to stall them for a while longer and shelter in the TARDIS while the wave passes by. However, Savage then collapses in agony, speaking in her own voice and begging the Doctor to save her before she succumbs to the Controller’s influence again. The Doctor compassionately promises to do all he can, apparently unaware that Savage is in fact still fully under Cyber control and is only trying to trick him...

Goddard catches Isherwood going through his belongings. Isherwood, still believing that the Cybermen are responsible for the temporal waves, believes that if he can strike a deal with the Cyber Controller he can learn the secrets of the future; however, Goddard warns him that Time isn’t a toy, and the Cybermen are not to be trifled with. Isherwood believes that Goddard is too young to know what he’s talking about -- but Goddard is older than he looks...

The Cyber Controller postpones Evelyn’s conversion while it monitors Savage’s progress. Oddly, however, it notices Evelyn’s fear and questions her about it. She tries to explain that the sense of adventure and the fear of dying is what makes life worth living, but the Controller no longer understands such concepts. Its sole purpose is to seed the Universe with Cybermen, and ensure the survival of its race. Evelyn senses a core of humanity within the Controller which still remembers what it was like to dream, but the Controller cuts off the conversation when Savage reports that she has successfully tricked the Doctor. Evelyn is horrified when Carey arrives, fully transformed into a Cyberman, and reporting for duty.

Goddard was born in the year 1927, and four days later, the Cybermen attacked Earth, releasing a technorganic virus which transformed every living thing on Earth into a cybernetic hybrid. All of the animals and most of the human race died from the shock, and the survivors became things like Goddard. Determined to save their people, a few rebels used a stolen Chronosphere to send Doctor Goddard to this nexus point, the point at which the Cybermen changed history. The Doctor demands an explanation for the vial which Isherwood found in Goddard’s tent, and he explains that it’s a reverse-engineered virus programmed to destroy the Cybermen’s implants. The Doctor, furious, informs Goddard that he’s participating in a paradox loop; if the Cybermen get hold of this virus, they will reverse-engineer it themselves, creating the “original” virus which Goddard is trying to prevent from being used. Goddard refuses to accept this, as he’s believed for all 24 years of his life that the Doctor is responsible for creating his nightmare world -- and when the Doctor tries to destroy the vial, Goddard strikes him, knocking him out.

Unable to see Goddard, Savage sees the Doctor fall down for no apparent reason, and demands an explanation from Isherwood and Renchard. When they tell her that Goddard is responsible, she has no idea what they’re talking about. Goddard stands by without intervening as Savage grabs Renchard and crushes his head to pulp, trying to force Isherwood to tell her the “truth”. She then drags the horrified Isherwood off to the time portal. The Doctor recovers, too late to save Renchard, but determined to save Evelyn and make Goddard pay for what he’s done. Goddard may consider himself to be a human rebel trying to save his species, but as far as the Doctor’s concerned he’s shown himself to have all the moral scruples of a Cyberman.

There are only minutes remaining before the temporal wave washes across the planet, and all in its wake will age to death within microseconds. Evelyn senses that, despite its emotionless facade, the Controller is near panic for some reason; nevertheless, the Controller orders its troops to take her for conversion. Savage then arrives with Isherwood, who desperately pleads for his life and offers to tell the Controller all it needs to know about the year 3286. It informs him that it cannot survive on the other side of the portal, however, and disconnects itself from the controls so it can show Isherwood exactly why not.

The Doctor and Goddard enter the temple, and Goddard destroys the Cyberman standing guard by the time portal. He then removes its face-plate, allowing the human beneath to die with his own face exposed. The Doctor and Goddard pass through the portal, and to Goddard’s surprise, half of the virus vanishes on the way through. The Doctor studies the hieroglyphs on the other side and works out how to operate the portal -- but he refuses to tell Goddard what he’s doing, as Goddard would enjoy it too much. He and Goddard then hide as the Controller and Isherwood arrive, and watch as the Controller sticks its hand through the portal. On the other side, it reverts to a fully humanoid hand. If the Controller passes through the portal it will become fully human once more. It is the last of its kind, and has limited resources on this side of the portal, which is why its captives have only been partially converted, using sub-standard parts. The Controller then reveals that it knows that the Doctor is hiding nearby -- but it is confused when Isherwood speaks to Goddard...

The Doctor claims to have no idea what Isherwood is talking about, and when Carey arrives, the Doctor tries to change the subject by informing him that Savage killed his friend Renchard. Unfortunately, Savage steps forward to silence him and walks right into Goddard before he can move. The Controller quickly deduces that “Goddard” is invisible, and the Cybermen alter their receptors and pick him up. The Doctor advises them to destroy the vial Goddard is carrying, as it contains a virus which will kill them all. The Controller knows that the Doctor will not use the virus, for they are the last of the Cybermen and Article Seven of the Time Lords’ own constitution forbids genocide -- but as the Doctor wonders how the Controller knows this fact, Savage attacks Goddard and takes the virus from him, intending to analyse it.

The Doctor reminds the Controller that it still needs the TARDIS to escape, and thus can’t kill him -- but the Controller now intends to use Evelyn as its pilot. Carey then announces that Goddard is not human, and Savage confirms that the vial contains a retrovirus engineered to destroy cybernetic implants. The Controller decides to change its plans, and has Savage and Carey take the prisoners to the conversion chambers. Isherwood will be converted at once, but the Controller orders Carey to delay converting Evelyn or the Doctor, as it is considering a new plan...

Evelyn’s conversion is halted just as it begins. As she tries to recover from the shock, Carey arrives and asks her about Renchard. For some reason he can’t stop thinking about the Doctor’s claim that Renchard is dead, and when Evelyn reminds him that Renchard was his friend, Carey sets off to question Savage and find out why she killed his friend. Unfortunately, he leaves Evelyn connected to the conversion machinery, and the Controller then orders Savage to resume the process -- and to convert Isherwood as well. As Savage reactivates the machinery, Carey arrives and confronts her, and as the two partial Cybermen battle, the Doctor sets off to find and rescue Evelyn. Savage kills Carey, but Goddard then kills Savage. He’s too late to rescue Isherwood, who begs Goddard to kill him before the conversion is complete -- but first he must warn Goddard of something that he’s learned from being connected to the data storage...

The Doctor disconnects the conversion machinery and pulls the dazed Evelyn out to safety. The Controller itself tries to prevent them from escaping, but Goddard arrives and holds it off. The Doctor warns Goddard that he’s sabotaged the portal so the temporal wave will wash through Cyber Control rather than out onto the planet’s surface -- but he and Evelyn then flee before Goddard can deliver his own warning. The Controller has already reverse-engineered the virus which Goddard brought, and has used the conversion machinery to infect Evelyn with it. She is now the carrier of the techno-virus which created Goddard’s timeline. Enraged, Goddard beats the Controller to death and removes its face-plate -- and as the temporal wave floods through Cyber Control and ages it into oblivion, Goddard is horrified to see that the Cyber Controller was once Evelyn Smythe...