In what may or may not be the distant future, the Thal starship Dyoni has found something horrific; whole planets have been devastated, entire civilisations wiped out by some unknown force. Professor Ptolem and his good friend Commander Ganatus are seeking answers, but they aren't prepared for what they find -- over a hundred billion gigantic life forms, clustered in a swarm larger than a planet, travelling through space at unimaginable speeds. The Dyoni is swept up in the monsters' wake, and barely survives... but it does emerge back in normal space, and the Thals find themselves somewhere they never expected to see again. The planet Skaro.

The Doctor finds Nyssa conducting repairs to the TARDIS console without his permission, but she assures him that she's only repairing the TARDIS' proximity alarm, so that they get a decent warning the next time they're about to collide with something. The alarm goes off almost at once, and a strange turbulence ripples through the TARDIS; the Doctor identifies it as a bump in the time track, and determines that they're being drawn towards a time corridor. Rather than allow the operators to capture him, the Doctor speeds towards the tunnel and bounces off. The TARDIS rebounds into normal space in a cultivated field, in which rape is growing three or four metres taller than it should. Moments after emerging from the ship, Nyssa is stung by one of the angry wasps buzzing about the field, but she dismisses the pain as unimportant and sets off with the Doctor to explore. Objects are buzzing through the sky overhead, too quickly for them to make out details -- but when the Doctor and Nyssa hear gunfire in the distance, that's all the detail they need. As they turn back towards the TARDIS, Nyssa spots a dead man nearby, with scars on his head and a bullet wound in his back. The Doctor studies the body, and finds a warrant card indicating that he was a sheriff from the state of Kansas. The date on the card suggests that they are on Earth circa 2157 AD... and the Doctor knows just what that means. Alien technology was grafted onto this man's head and removed by the same people who killed him, and the Doctor and Nyssa must get back to the TARDIS. Now.

Much further into the future, two of the last human beings on Earth watch as one of their alien visitors trudges through the blizzard outside their shelter. Albert, who is descended from British royalty, is grateful for the food and medical supplies which the Thals have provided, but the lower-class Dolores is less trusting. What's to stop the Thals from taking off again and leaving the humans in the lurch? Meanwhile, Ptolem finishes collecting his soil samples, only to learn that they may not be necessary after all. Ganatus reports that they've finally detected the Doctor's TARDIS -- but the Doctor has evaded capture and materialised somewhere on 22nd-century Earth. Ptolem, knowing the Doctor's reputation, guesses that he's arrived in 2158 AD, a rather important year... and a rather dangerous one.

Just as Nyssa and the Doctor get back to the TARDIS, another sheriff steps out of the grain and holds them at gunpoint. But this sheriff still has alien technology grafted onto his head, he speaks in a slurred, dragging voice, and he doesn't even seem to notice the wasps flying about his head and stinging him repeatedly. Unsure what to make of his new captives, he calls in backup... and the Doctor must watch helplessly as one of the buzzing shapes descends from the sky, and is revealed to be a dented, battle-scarred Dalek on a hover-disc. Surrounded by angry wasps, the Dalek demands that the Doctor and Nyssa identify themselves, but instead they make a break for it, and miraculously manage to get inside the TARDIS before the Dalek or its Roboman servant can shoot them.

While Nyssa fetches a first aid kit for her arm, the Doctor dematerialises... but in his haste he's forgotten why they arrived here in the first place, and the TARDIS gets caught in the time corridor almost immediately. The Doctor can't break free, and he's certain that there will be Daleks waiting on the other end. Nyssa suggests trying to break free anyway; they won't change their temporal destination, but might cause a spatial deviation. The Doctor tries doing so, and thus materialises not in the Thal base, but the human shelter. He and Nyssa emerge to find themselves in an concrete bunker, clearly deep underground and under enormous pressure. Nyssa fears that there might be more Daleks out there, but the Doctor assures her that the invasion ended some time ago, and that he participated in the Daleks' defeat. Albert and Dolores arrive to investigate the mysterious vworping noise, and are surprised to find two strangers in the bunker. But not as surprised as the Doctor is when the two humans mention that there are Thals nearby.

Ptolem prevents the Daleks from exterminating the mutant; he's been granted full authority by the Dalek Emperor himself to do whatever is necessary, and he intends to study this creature's development from the start. The Daleks are obviously itching to kill it, but even they must concede that the Doctor's capture is not certain; Earth in 4250 is not a very safe place. They must therefore allow Ptolem to continue his experiments as he sees fit. The Daleks reluctantly return to Skaro, and Ptolem and Ganatus have the mutant restrained within a containment field. As soon as Ptolem administers a nutrient drip, the creature revives and begins to grow at an incredible rate. Ganatus remains pessimistic about their chances for survival, but Ptolem informs him that he has a form of insurance in case the Daleks turn on them. But he will say no more; instead, he goes for some much-needed sleep.

Dolores and Albert confirm that the Earth was devastated by a global disaster over thirty years ago, when Albert was still a child and Dolores had yet to be born. Professor Karl Hendrick is the only man alive who can answer the Doctor's questions, so Dolores takes the Doctor to speak with him while Albert takes Nyssa to get her wasp sting treated. The Doctor is shocked when Dolores casually reveals that the twenty or so people in this shelter are the last humans left alive on Earth. The Thals scanned the entire planet when they first arrived, and they seemed surprised to find even this one human bunker still intact... which suggests to the Doctor that they were looking for something else. This doesn't surprise Dolores, who doesn't trust the Thals and believes that the human race is doomed. Karl claims that there are other colonies out there, but if this is so, why hasn't anybody returned to Earth to check on them?

Albert leads Nyssa to the bunker's library; all they have are printed texts, as their computers stopped working some time ago. He seems distracted, however, and leaves Nyssa alone with the first aid kit without telling her where he's going. Disturbed, she applies the medication to her own arm, and then goes off in search of Albert -- only to find him talking to himself in the darkness. Or perhaps he's talking to someone else, for he's telling them about the arrival of two strangers in a blue box called the TARDIS. Nyssa rushes off to warn the Doctor that their new acquaintances are working with the Daleks, only to run into Dolores, who isn't sure why Nyssa is so panic-stricken. She agrees to take Nyssa to the Doctor -- but then Albert arrives, and tries to stop them. Realising that something is genuinely wrong with Albert, Dolores gives him a good kicking, and heads off with Nyssa to warn the Doctor and Karl.

The Doctor has met Karl Hendrick, a suspicious and moody man who prefers to live in darkness. He doesn't trust the Doctor at first, but eventually accepts that the Doctor only wants some answers about the disaster, and the Daleks. Karl vaguely recalls stories of creatures called Daleks, but he's quite sure that they aren't responsible for the disaster. As the Doctor's eyes grow accustomed to the darkness, Karl takes him to see the corpse of one of the creatures which laid the Earth to waste -- a monstrous insectoid over a hundred metres in length, with wings like metal shields. These creatures descended upon the Earth, draining all of the life out of the world, consuming all of the plants, nutrients, minerals, and micro-organisms in the soil. They absorbed all energy directed against them; just to touch them meant death. For some reason they began to die off, but by that time the Earth was already dead, and soon the human race will be as well. The Doctor's questions remain unanswered; what does this have to do with the Daleks, and why do Karl and Dolores instinctively distrust the Thals, one of the most peaceful races in the galaxy? There's something terribly wrong here...

The situation on Skaro is grave, as the Mutant Phase maintains its assault on the planetary defense barriers. All available power resources have been diverted to the defense grid, but the mutants are simply absorbing the energy. When the Daleks' agent on 43rd-century Earth alerts them to the Doctor's presence, the Dalek Emperor therefore despatches a squad to capture him immediately. The Daleks' arrival awakes Ptolem from an uneasy sleep, and although they're furious to see that he's studying a captured mutant, they're unable to stop him. However, as important as Ptolem's experiments may be, they have orders to take him to the Doctor at once -- and this time, they really will exterminate him if he disobeys. Ptolem and Ganatus have no choice but to set off through the winter storm with the Daleks, but soon after they've gone, a crisis occurs. The mutant has been growing at a fantastic rate, and it starts to break through the defense screens in the laboratory...

Nyssa is horrified by the Daleks' cold-bloodedness, even more so when the Daleks announce that Albert is now surplus to requirements and exterminate him. They return to the Thal base with their prisoners, taking the TARDIS with them. There, they intend to force the Doctor to help them, although Ptolem insists that he be allowed to explain the situation to the Doctor so that he will help of his own free will. But the threat becomes obvious when the laboratory defense screens collapse and the mutant breaks out. The Doctor recognises it as one of the monsters which Karl showed him, and just as Karl had claimed, it sucks the life out of everything that gets near it. The other Thals in the base are already dead, and the Doctor, Nyssa, Ptolem, Ganatus and the few surviving Daleks are forced to retreat into the TARDIS. There, Ptolem tells the Doctor that the monster outside is a Dalek... or rather, it's what the Daleks are becoming. Some random infection in the Dalek gene pool is transforming them into the Mutant Phase, and they have no idea how to stop it.

The Doctor is still wary of helping the Daleks, but Ptolem impresses upon him the sheer scale of the horror. The mutation robs the Daleks of all higher brain functions; the Mutant Phase is a swarm of mindless, destructive beasts, consuming whole civilisations and laying waste to the Universe. The Earth is the only planet on which the creatures have died out, but Ptolem is no closer to understanding why; and if he can't stop the Mutant Phase, the people of the Universe are doomed. The Daleks are evil incarnate... but the Mutant Phase is worse. The Doctor is deeply concerned; this is not how things should be, and he's starting to believe the release of temporal energy that rippled through the TARDIS when he first encountered the Daleks' time corridor was even more serious than he'd thought...

The situation on Skaro is desperate; the mutants will be through the failing defense barriers within hours. The Doctor advises Ptolem to take a look at Nyssa's arm, before being ushered off to an audience with the Dalek Emperor. The Emperor informs him that Ptolem has analysed the Daleks' genetic records extensively, and could detect no impurities before the Earth year 2158. The Daleks regularly extract genetic material from their soldiers in order to facilitate operations at their reproductive factories -- and an undetected infection in one Dalek could, theoretically, spread to the entire race in time. The Doctor realises that the Emperor wants him to go back in time to stop the Mutant Phase before it starts, and although under ordinary circumstances he'd rather sacrifice himself than be forced to change history -- particularly for the Daleks' benefit -- he's starting to realise that these circumstances are anything but ordinary. He has no choice but to accept the Emperor's mission.

Ptolem becomes intrigued when Nyssa explains that she was stung by a wasp on Earth in 2158; however, his laboratory is in a vulnerable sector of the city, and he, Ganatus and Nyssa must work under the supervision of increasingly nervous Daleks. Ptolem takes tissue samples from Nyssa's wound and explains why the Daleks need the Doctor; they are unable to change history themselves, as they no longer have the power to reach back that far in time. But at long last, Ptolem thinks he has a solution. The Mutant Phase feature certain insectoid characteristics, and Ptolem doesn't think it's a coincidence that Nyssa was stung by an insect in the same year that the first impurities appeared in the Dalek genetic database. The wasp laid eggs in Nyssa's flesh when it stung her, and after Ptolem burns out the affected area and heals her arm, she helps him to analyse the samples -- and confirms a partial match between the wasp eggs and the mutant DNA. Before they can analyse their results, the mutants finally break through the Dalek defense barriers. Ptolem saves his research onto a data crystal, but while Ganatus and Nyssa retreat to the TARDIS, Ptolem lags behind to collect his "insurance"...

The Dalek city will be completely overrun within about 150 rels, and for the first time in his memory, the Doctor actually feels sorry for them. The Emperor sends him back to the TARDIS to complete his mission, informing him that Ptolem has made a vital discovery. It's a strange experience, having Daleks laying down their lives to get him to safety. Once safely within the TARDIS, Ganatus urges the Doctor to dematerialise immediately, for the Dalek Emperor intends to destroy Skaro rather than permit the Mutant Phase to consume or corrupt him. Although unsure where Ganatus got this information from, the Doctor heeds his warning and dematerialises, to observe the end of Skaro from what he hopes will be a safe distance. As the Mutants overrun the Emperor's domain, he initiates total transference, severs the time corridor, and destroys the planet. The shockwaves ripple out through Time, and as the TARDIS shudders in sympathy, Ganatus passes out in a dead faint. The Doctor fears the effect the collapse of the Daleks' time corridor will have, but he stops himself from saying any more and instead helps Ptolem to carry Ganatus to a guest room. Nyssa sorts through Ptolem's belongings, searching for the data crystal... and is rather surprised to find something else as well.

The next morning, Nyssa finds the Doctor still working in the TARDIS laboratory. He's been up all night, and is no closer to a solution. Somehow a Dalek absorbed DNA from the same type of wasp that stung Nyssa, but how could a wasp possibly penetrate the polycarbide armour and other defenses to sting the Dalek's organic being? And then there's Ganatus -- why did he faint and why has he still not woken? Nyssa urges the Doctor to get some rest... but first, there's an important question she's been trying to work up the courage to ask. She knows that the Doctor has been hovering in the TARDIS in order to put off the decision to land... but she also knows that he's seriously considering trying to change history. And if he refused to do so in order to save Adric, why is he doing it to save the Daleks? The Doctor is clearly uncomfortable; he trusts Nyssa implicitly, but doesn't know what her future holds, and it's possible that after she leaves his company she may encounter others, who may force her to tell them about her time with him. And there are certain facts about the nature of the Universe which the Time Lords must keep to themselves. All that he's willing to say is that sometimes, paradoxes occur in Time -- and under certain circumstances they could unravel the very fabric of the Universe...

Somehow Ptolem finds it easier to talk to Ganatus while his friend is unconscious. Ever since they started working with the Daleks, a distance has grown between them. Even now, Ptolem is keeping an important secret from his friend... Ganatus starts to awaken, and Ptolem goes to fetch the Doctor -- but the TARDIS starts to shake and the cloister bell tolls. The tremors also interrupt Nyssa as she works in the laboratory; she's had an inspiration, and instead of continuing to analyse the wasp DNA she's searched the TARDIS historical data banks for any references to wasps after the year 2158. She joins the Doctor and Ptolem in the console room, where she reveals that the vegetation in the field where the TARDIS had materialised had been genetically modified. She now knows what killed the Mutant Phase on 43rd-century Earth. But the matter may soon become academic; the Emperor's last action was to boost power to the time corridor and force its entrance back to 2158, in order to force the Doctor to land. But the time corridor really is collapsing now, and the TARDIS is trapped inside...

The Doctor doesn't think he can break free of the collapsing time corridor -- until, much to his surprise, he does. The TARDIS materialises in the exact same spot as before, right to the atom, and the Doctor, Nyssa and Ptolem watch on the scanner as events unfold just as before. The Doctor and Nyssa's past selves are captured by a Roboman sheriff, who calls for backup, and a Dalek arrives -- a dented and battle-scarred Dalek, its casing breached by gunfire, enough for a single wasp to crawl through... Having seen enough, the Doctor shifts his own TARDIS 500 metres west, out of harm's way. Now they've established the origin of the Mutant Phase, and Nyssa knows what destroyed it on 43rd-century Earth; traces of a particular pesticide, which she found in Ptolem's soil samples. The plants in this field have been genetically modified, not only to grow taller, but to release a chemical agitant which causes the wasps in the field to become more aggressive. The wasps thus kill more of the caterpillars which would normally feed on the plants. But the TARDIS data banks indicate that the wasps became too aggressive -- and after the Daleks were driven away from Earth in 2167, there were widespread wasp attacks, culminating in the deaths of over 500 people in a single swarming in 2172, and the use of the GK-50 insecticide to wipe out the swarms. Since the Mutant Phase is partly descended from the same strain of wasp, the traces of GK-50 in Earth's soil killed them off when they fed from it.

The infected Dalek returns to its base to report the incident with the disappearing blue box. Its commander concludes that the damaged Dalek is experiencing perceptual distortions, and orders it back to the remoulding bay for repairs to its outer casing... and for cell analysis and donation. It's beginning... or is it?

The Doctor and Nyssa synthesise some GK-50 in the TARDIS laboratories, but Ptolem doubts that the insecticide will be effective against the Mutant Phase this early in its development. He would prefer simply to kill the infected Dalek, but the Doctor refuses; they're in a damaged spatiotemporal nexus, and any action they take could be disastrous. The infected Dalek may have another role to play in the web of Time; for example, it may be destined to kill someone who would otherwise change history if he survived. They must leave this era essentially as they found it. Ganatus arrives in the laboratory, apparently fully recovered, but as Nyssa presents the loaded injection probe, Time itself seems to freeze and ripple about them. Only the Doctor and Nyssa, both seasoned time travellers, can perceive the effect -- the beginning of a paradox which threatens to destroy the Universe. The Doctor had thought that the crisis was caused when he bounced off the Daleks' time corridor, ended up in a time and place where he had no right to be, and inadvertently lured a damaged Dalek into a swarm of wasps, creating the Mutant Phase. But he was wrong... the real nexus point of the paradox is Ganatus.

Before he can explain further, the time distortion ceases. Ganatus and Ptolem have noticed nothing, but Ganatus, asking Nyssa if she feels well, offers to take the injection probe from her. The Doctor tries to stop him, but fails; Ganatus seizes the injection probe and puts it to the Doctor's neck, now speaking with the voice of the Dalek Emperor. The Emperor never trusted Ptolem to work unsupervised, and linked his own mind to that of Ganatus in order to keep him under observation. When Skaro was destroyed, the Emperor's last act was to transfer his mind completely into Ganatus' body. There is nothing of Ganatus left any more; only the Emperor exists, and he now intends to insure the Daleks' triumph in this time zone and all others. He forces the Doctor out of the TARDIS, and orders him to use a DNA tracker to locate the infected Dalek; however, the Doctor refuses, and deliberately smashes the tracker in order to let events take their natural course. As it happens, Dalek patrols are still searching the area for the freedom fighters who killed the first Roboman patrol, and they capture the Doctor, the Emperor -- and the TARDIS.

Inside the TARDIS, Nyssa and Ptolem appear helpless... but that's only because Ptolem hasn't told Nyssa about his "insurance policy" yet. Little by little, working under the Daleks' metaphorical noses, Ptolem has developed a retrovirus which would have been useless against the Mutant Phase... but which will have a devastating effect on ordinary Daleks. All he has to do is step outside and break his capsule, and within two generations there will not be a Dalek left in the Universe. Nyssa understands enough of what the Doctor has told her to know that they can't risk interfering with history on such a scale, but Ptolem is adamant; he'll release the virus, the first chance he gets...

The Daleks take their prisoners back to base, where the Emperor claims to be a traveller from the future, here to help the Daleks avoid a catastrophe. The Daleks don't believe him, until he actually starts to speak with the voice of the Dalek Emperor. This gets their attention, and when he reveals details about the invasion which only the Emperor could know, this seems to confirm his story. Confronting a Dalek with the impossible isn't easy, however, and he only confuses matters when he tries to explain that the Doctor will arrive in nine years and defeat the Dalek invasion -- but that it won't do any good to kill him now, because he will still have already done so. Realising that he's on a hopeless tack, the Emperor returns to the matter at hand -- warning the Daleks about the Mutant Phase, and giving them the pesticide which will eliminate the infection. The commander confirms that there is a damaged Dalek in the repair section -- and that they have already detected alien genetic material in its DNA and are preparing to extract it. The Doctor finally puts the pieces together...

The TARDIS is brought into the base for study, and on the scanner, Nyssa and Ptolem see the Doctor and Ganatus surrounded by Daleks, apparently under threat of extermination. This is enough for Ptolem, who overpowers Nyssa and rushes outside with his retrovirus capsule. The Doctor, meanwhile, tries to stop the Emperor from handing over the injection probe, telling him that Ptolem was right; the pesticide won't affect this early stage of the mutation. The Doctor isn't the nexus of the time paradox, the Emperor is, and by supplying the Daleks with a faulty pesticide he'll seal their fate forever. As the Emperor hesitates and Ptolem emerges from the TARDIS with his retrovirus, the Dalek commander gives up trying to understand what's happening and orders his Daleks to kill them all. But it's the Emperor who makes the vital first move, by throwing the injection probe to the ground and smashing it, spilling its contents away.