The TARDIS materialises in an alleyway, and the Doctor and Rose emerge, unaware that they’re being observed. The Doctor warns Rose that since the cylinder was jumping time tracks so erratically, it probably arrived three or four weeks earlier. Rose assumes that the Doctor is going to scan the city for signs of alien technology, and is disappointed when he points out that all he needs to do is find someone, use his psychic paper to pose as a representative of the Ministry of Asteroids, and ask whether anything fell out of the sky in the middle of London. Hearing music and the sounds of a crowd behind a nearby door, the Doctor uses his sonic screwdriver to break in; however, as he enters, Rose hears the sound of a child calling out for its mummy, and turns to see a young boy in a gas mask standing on a nearby rooftop.

The Doctor finds himself in a smoky jazz lounge, where a singer is crooning It Had to be You. Following the song, the Doctor joins in the applause, and then takes the stage and asks the audience if anything has fallen from the sky recently. The audience bursts out laughing, and as the Doctor tries to understand their reaction, air-raid sirens begin to wail and the audience promptly evacuates to the shelters. The Doctor finally notices a war poster on the wall, and realises why his question caused such hilarity -- he’s landed in the middle of the Blitz. Outside, Rose climbs a fire escape to the roof, but is unable to get up to the child until a rope drops down to her. Unsure where the rope came from, Rose nevertheless starts to climb -- and discovers, too late, that it’s attached to a barrage balloon that has come free of its moorings. The balloon drifts away from the building, leaving Rose dangling precariously in mid-air, desperately clutching onto the rope as German planes hurtle through the air around her. Suddenly, wearing a great big Union Jack like a bull’s-eye on her T-shirt doesn’t seem like such a good idea.

The Doctor rushes out of the club only to find that Rose has vanished. As he complains to a nearby cat that his companions are always wandering off against orders, the phone in the TARDIS’ exterior cubby-hole starts to ring. This should be impossible, since it’s not a real phone. A teenage girl arrives in the alley and warns the Doctor not to answer the phone, but she vanishes while his back is turned, before he can find out what she knows. He answers the phone anyway, and hears a child’s voice, calling for its mummy. The signal then cuts off. Puzzled, the Doctor follows the sound of clattering to a nearby home, where he sees the Lloyd family evacuating to the air-raid shelter in their garden -- much to the irritation of Arthur Lloyd, who’s frustrated that the Germans always interrupt his dinner. As soon as the family is inside the shelter, the girl from the alley pops out of hiding and enters their house, where she begins stealing all the food she can fit into a small sack.

Elsewhere, Rose’s plight is being observed from a nearby officers’ club by Captain Jack Harkness, who is apparently an American flight officer -- but who’s using a pair of binoculars far too advanced to be from the 1940s. As the other officers prepare to evacuate the club and Jack’s fellow officer, Algy, departs for a rather odd stint of guard duty, Jack sets off to rescue Rose. Not too long afterwards, Rose finally loses her grip on the rope and falls, screaming -- but one of the searchlights sweeping across London transforms into a tractor beam and catches her. The computer aboard Jack’s ship detects Rose’s cellphone, which indicates that she is not native to this era, and Jack contacts the shaken Rose, telling her to switch off the cellphone so it won’t interfere with his instrumentation. Once she does so, he uses the tractor beam to lower her into his ship. The descent has made her giddy, and her close proximity to the attractive Jack doesn’t help; in any case, she faints.

The Lloyd family has abandoned their dinner on the dining room table, and the teenage girl calls in a crowd of homeless children to take advantage of the windfall. She carves the turkey for them, presiding over the gathering like a mother and chastising young Ernie when he comments that the family must have purchased this food on the black market. The Doctor then arrives and causes a brief panic when he takes a seat with the children, but the girl calms them down, realising that the Doctor isn’t supposed to be here either. The Doctor learns that these children had been evacuated from London but returned because they couldn’t live with the people they’d been billeted with; the teenage girl, Nancy, has been keeping an eye out for them, and whenever a family abandons their dinner during an air raid, she calls in the children to feast. It’s dangerous to be out under these circumstances, but the Doctor is impressed with her audacity.

Nancy demands to know why the Doctor has followed her here, and the Doctor in turn questions her about the mysterious telephone call. He also draws a sketch of the mauve cylinder and asks the children if they’ve seen it. Nancy seems to react oddly to the drawing, but before the Doctor notices this, a young child begins knocking at the window, calling out for its mummy. The Doctor draws the curtain aside to reveal the same boy that Rose saw earlier, still wearing his gas mask. For some reason, Nancy seems terrified of the child, and she bolts the front door and orders the other children to flee out through the house’s back exit. The Doctor tries to understand what’s got Nancy so frightened, but all she will tell him is that he mustn’t let the child touch him. This isn’t an ordinary child; he’s “empty”. The telephone rings, and the Doctor answers it and hears the boy on the other line. Nancy slams the receiver back down, but then the boy’s voice starts to come out of the radio and a nearby clapping-monkey toy. Nancy flees, but the Doctor remains to speak to the boy, who is reaching through the mail slot, revealing a deep scar on the back of his hand. The Doctor tells the boy that his mummy isn’t here, and when he opens up the door to let the boy in, he finds that the street is empty.

Rose awakens aboard Jack’s ship, and the dashing young man hands her a paper that apparently identifies him as an American volunteer in the Royal Air Force’s 133 Squadron. However, she recognises it as the same kind of psychic paper that the Doctor uses -- and when she returns it to Jack, he finds out that she considers herself available even though she’s got a sort-of boyfriend. Seeing that Rose is injured, Jack heals the rope burns on her hands with a cloud of nanogenes, tiny medical devices that swarm over her skin and instantly fix the damage. He then lowers a ramp and invites her up onto the “balcony” to discuss business over champagne. Rose follows him out onto the hull of his ship to discover that it’s invisible -- and is tethered to Big Ben. Jack flirts confidently with Rose as they drink champagne, and though she points out that these aren’t the best circumstances to be hitting on her, she seems disappointed when he stops. He thus puts on Glenn Miller’s Moonlight Serenade and dances with her while explaining that a fully armed Chula warship, the last of its kind, has crashed somewhere in London. He knows where it is, and is willing to sell that information to Rose, whom he believes to be a Time Agent like he was before he went freelance. However, there’s a deadline, because the ship will be destroyed by a German bomb within two hours. Rose, quite captivated by the charming young man, nevertheless tells him that he should be discussing terms with her companion. She is pleased when Jack decides to track down the Doctor by scanning the city for alien tech.

The Doctor follows Nancy to her shelter in an abandoned railway engine, and demands to know why she’s frightened by the child in the gas mask. He suspects that this mystery is related to the crash of the mauve cylinder, and Nancy finally admits that the cylinder fell on the other side of Limehouse Green station and is now being guarded by the military. To his surprise, she also tells him that if he wants to find out what’s going on, he’ll have to speak to “the doctor.” The Doctor sets off to check out the crash site, but as Nancy had told him, the cylinder is under a tarpaulin, behind a fence, guarded by soldiers. Nancy again advises him to speak to the doctor in the nearby hospital. As she sets off to collect more food from the Lloyds’ house, the Doctor asks her one last question. Perhaps from personal experience, he’s deduced that she’s mothering the other children because she’s lost someone close to her and is trying to make up for it. She admits that her little brother Jamie was caught in an air raid, the night the cylinder fell, when he followed her out looking for food. The Doctor sympathises for Nancy’s loss, but admits that he’s impressed by her strength, the same stalwart spirit that enabled the British to make a stand against Hitler and stop the German advance in its tracks. He and Nancy go their separate ways... unaware that the empty child is here and is following Nancy.

The front gates of the hospital are padlocked, but the Doctor breaks in with his sonic screwdriver. This is Albion Hospital, which the Doctor has visited before, and as the Doctor explores, he finds each ward full of lifeless bodies, one to a bed, all wearing gas masks. He then meets the one living inhabitant of the hospital, the elderly Dr Constantine; this is the doctor to whom Nancy was referring. Constantine claims that the hospital is full of bodies, and that the bomb is responsible for all of this -- yet none of the patients were caught in the blast, and according to Constantine, they aren’t really wearing gas masks. He invites the Doctor to examine the bodies, but warns him not to touch the patients’ flesh. The Doctor scans the bodies with his sonic screwdriver, and discovers that each one has identical injuries: head trauma, partial collapse of the chest cavity and a scar on the back of the hand. Also, the gas masks appear to be fused to the flesh, yet with no sign of burning. Constantine -- who also has a scar on the back of his hand -- reveals that the bomb only took one life, but every doctor and nurse who touched the patient acquired the same injuries. Within a week, the symptoms had spread throughout the entire hospital, as if the physical damage to the bodies was some sort of plague.

The bodies have no heartbeat, and show no signs of life -- but when Constantine kicks aside a trash can with his cane, his “patients” react to the noise, sitting up as if in alarm. Constantine, who lost his entire family in the war, remained to care for his patients, but he has no idea what to do for them, and he suspects that the British intend to blow up the building and blame it on the Germans. It’s too late, however, as he’s heard that isolated cases of the same “plague” are breaking out all over London. He tells the Doctor to visit room 802, where they took the first patient, and to try to convince Nancy to tell him what else she knows; what’s happening here is somehow related to her brother. But before he can tell the Doctor anything more, he begins to choke, and calls out for his mummy -- and as the Doctor watches, appalled, a gas mask seems to grow right out of Constantine’s face.

As Constantine slumps lifeless in his chair, the Doctor hears Jack and Rose calling out to him. Rose introduces Jack to the Doctor, who is rather put out to learn that Rose, embarrassed not to know his name, introduced him to Jack as “Mister Spock.” Rose also explains that Jack wants to sell them a Chula warship, and that they’ve got less than two hours before a German bomb destroys it. However, Jack’s confident facade crumbles when the Doctor shows him the bizarre bodies in the ward. Jack insists that he has nothing to do with this, but when the Doctor reveals that this all started around the crash site and demands to know about the warship, Jack caves in and admits that it’s just the empty shell of an ambulance. When Jack spotted the TARDIS, he assumed that its occupants were Time Agents, and he threw a random piece of space flotsam towards them, intending to trick them into thinking it was valuable, fleece them and be on his way before they realised they’d bought a piece of junk. But if the cylinder really was empty, then what’s rewriting the DNA of the gas-masked patients? And why?

Nancy returns to the Lloyds’ house, but moments after she enters the dining room, the radio switches itself on and the empty child speaks through it, begging his mummy to let him in. Terrified, Nancy hides under the table as the child enters the house, looking for his mummy. Nancy tries to flee when the child’s back is turned, but the child simply points his finger at the door, which slams shut and locks itself. The child then advances on the terrified Nancy, who knows exactly who this child is: it’s her brother, Jamie, and he’s supposed to be dead. As Jamie advances on her, the patients in the ward at Albion Hospital all sit bolt upright and get out of bed, calling for mummy. The Doctor warns Rose and Jack not to let the patients touch them, but the zombies surround them, backing them up against a wall...

The Doctor steps forward and addresses the gas-masked zombies like a cross parent speaking to a disobedient child. To his relief, when he orders them to return to their room at once, they bow their heads sadly and return to their beds. Once the immediate crisis passes, Jack regains some of his swagger, and insists again that whatever is happening here isn’t his fault. He’s played this type of confidence trick before: throw a piece of harmless space junk past a Time Agent, claim that it’s an important artefact and get a down payment on it, and then let a German bomb destroy the vessel before the mark realises that it’s actually worthless. The London Blitz is perfect for that sort of con, as is the destruction of Pompeii. He insists that the vessel was an empty medical transporter and that he even programmed the flight computer to make sure it didn’t harm anyone when it landed. But the Doctor remains convinced that there’s a connection between the ambulance and whatever’s happening in this hospital.

Jamie, the empty child, has also been affected by the Doctor’s demand, and has sadly retreated from the Lloyds’ house, leaving the shaken Nancy behind. Overcome with emotion, she remains huddled on the floor of the dining room until the all-clear sounds, and by the time she pulls herself together, the Lloyds are on their way back into their house. They soon realise that Nancy has been looting their house, and Arthur holds her in the living room while waiting for the police to arrive. But Nancy has been scouting out this house for some time, and she knows Arthur’s secret. His neighbours think he has more food than them because his wife’s been carrying on with Mr Haverstock, the butcher... but actually, it’s Arthur who’s been doing so. Nancy demands a torch, a pair of wire cutters, and more food from the pantry, and Arthur caves.

The Doctor takes Rose and Jack to room 802 and asks Jack to blast open the door; he could use his sonic screwdriver, but he wants a closer look at Jack’s gun. He recognises it as a sonic blaster with a digital blast pattern, originating from the 51st-century weapons factories of Villengard. Jack is surprised to learn that the Doctor is responsible for blowing up the weapons factories; now they’ve been replaced with banana groves. The Doctor, Rose and Jack enter room 802 to find that it’s an isolated ward; the window has been smashed open, as if something very powerful and angry escaped, and yet the room contains a child’s toys and drawings. The Doctor plays a tape of Dr Constantine’s interview with his patient; all the boy can speak of is his mummy, and he doesn’t seem to understand where she’s gone. The Doctor tells Rose and Jack about the children he met earlier; one of them must have been affected by whatever was in the “empty” medical ship. The boy is frightened, angry, and more powerful than he realises -- and they can still hear his voice, even though the tape ran out 30 seconds ago. Too late, the Doctor realises that the child has done exactly what he told it to do; he’s gone back to his room, this room, and he’s standing between them and the exit.

Jack points his gun at the child, only to discover that he’s now holding a banana and that the Doctor has the gun. The Doctor disintegrates a hole in the wall, and as soon as he, Rose and Jack have leapt through, Jack grabs back his gun and reintegrates the wall. The child impossibly punches his way through, and the gas-masked zombies then pour into the corridor from all directions, blocking the others’ escape. Effectively, every living being in this hospital is now the same entity, and they’re holding the Doctor, Rose and Jack here until the child can get to them. Rose uses Jack’s gun to disintegrate a hole in the floor, which Jack then reintegrates once they’ve fallen through -- but they’ve fallen into a ward full of gas-masked patients, and now the battery in Jack’s sonic disruptor has run out of power. The Doctor, Rose and Jack flee from the ward and take shelter in an empty office; it will take some time for the child to find them again, but there’s no way out without being caught. Or so it seems until the Doctor and Rose notice that Jack has vanished into thin air.

Nancy finds the other children hiding in an abandoned house, and is upset with them for returning to the same place when she’s told them to keep moving. Ernie apologises, but explains that they needed to hide where Nancy could find them. However, Nancy tells him that it’s time for him to start thinking about what might happen if she fails to return. Ernie notices that she’s carrying wire cutters, and she admits that she’s going back to the bomb site where the empty child was killed. The other children are terrified that he’ll kill her and then come for them, but she tells them that there are things they don’t know, and insists that the child is only after her, not them. Even as she speaks, the typewriter that young Jim was using to write a letter to his dad starts to type by itself, in block capitals: “ARE YOU MY MUMMY?” Nancy leaves, telling the children to take care of themselves, eat their greens and chew their food.

Jack has used his emergency teleport to return to his ship, but it’s going to take some time for him to bypass its security codes and rescue Rose and the Doctor as well. He contacts them by using his om-com, which allows him to speak through anything with a speaker grille -- just like the child, who speaks to them through the same radio, telling them that he’s coming to find them. Jack blocks the signal with Moonlight Serenade and gets back to work. The Doctor tries using his sonic screwdriver on the concrete walls to shake the bars free of the window, but Rose is confident that Jack will come to their rescue. She claims that Jack is a lot like the Doctor, except that he knows how to dance. The Doctor is put out by Rose’s assumption that he never dances, and Rose, amused, turns up the volume on the radio and invites him to show her his moves. He takes her hand, but is distracted when he sees that her hands show no sign of injury even though she was hanging from a barrage balloon thousands of feet above London. Rose explains that Captain Jack healed her wounds, and notes that the Doctor actually seems a little jealous.

The Doctor and Rose begin to dance awkwardly, only to find that they’re aboard Jack’s ship. Jack is amused to see that they’re so wrapped up in what they were doing that they failed to notice when he teleported them aboard. The Doctor notes that it took Jack a long time to bypass what are supposedly his own security protocols, and Jack admits that this ship wasn’t originally his. The Doctor identifies it as a Chula ship, just like the medical transport that Jack was trying to sell to him, and when he snaps his fingers, the cloud of nanogenes that healed Rose’s hands now fixes the burn he got from the overheating TARDIS console. The nanogenes only activate when the ship’s bulkheads are closed, automatically checking out the passengers and fixing any damage to their bodies. Disturbed, the Doctor orders Jack to get the ship’s nav-com back online and take them to the crash site. Jack realises that the Doctor doesn’t trust him, but admits to Rose that the Doctor might have good reason; the Time Agency took two years of Jack’s memories away from him while he was still an Agent himself, and he has no idea what he did in that missing time.

Nancy easily breaks into the bomb site, but is caught by soldiers as she tries to examine the “bomb” under the tarpaulin. Algy, Jack’s friend from the officers’ club, takes Nancy into a nearby shed, handcuffs her to the bench, and assigns a soldier named Jenkins to keep an eye on her while the other soldiers scout out the perimeter to determine whether she was alone. Nancy sees that Jenkins is ill and has a scar on the back of his hand, but despite her terrified pleas, Algy leaves her locked up in the shed with Jenkins. Nancy begs Jenkins to release her before it’s too late, but it already is; Jenkins forgets even his own name, and begins to choke as something forces its way up through his throat...

The Doctor, Rose and Jack arrive at the crash site, and Rose offers to distract the guard on duty; however, Jack recognises him as Algy, and tells Rose that she isn’t exactly his type. Rose is a little shocked when Jack sets off to “distract” Algy himself, and the Doctor explains that the people of the 51st century are a bit more flexible when it comes to... dancing. However, when Jack greets Algy, the disoriented Algy asks if Jack is his mummy, and then falls to his knees as his face transforms into a gas mask. The Doctor and Rose rush forward to stop the stunned Jack and the other soldiers from touching Algy, but the Doctor now knows that it would make little difference; the infection has gone airborne, and it could strike at any time. There could be only hours before the entire human race is affected.

Sirens begin sounding, marking the start of another bombing run -- the one during which the warship is due to be destroyed. However, the Doctor hears singing from the nearby shed, and investigates to find the terrified Nancy singing a lullaby to the gas-masked Jenkins. The Doctor frees her and takes her to the cylinder, which Rose explains to the astonished Nancy is an ambulance from another planet. The soldiers have been trying to open it up, assuming it to be a Nazi secret weapon, but only Jack knows the entry code. However, when he punches it in, an alarm begins to sound; since the cylinder crashed, its emergency protocols have been activated. And in Albion Hospital, the gas-masked zombies rise from their beds and march towards the crash site...

The Doctor orders Jack to secure the gates and gives Rose his sonic screwdriver, telling her to use setting 2428-D to reattach the barbed wire that Nancy cut through. Nancy, still trying to understand what’s happening, scoffs when Rose claims to be a time traveller from London’s future -- not because of the time-travel claim, but because she can’t believe her city has a future. Rose assures Nancy that, impossible as it may seem in the middle of the Blitz, the British will in fact win this war. She and Nancy then return to the cylinder just as Jack manages to get it open, revealing that it’s empty, just like he claimed. Except that the Doctor points out that Chula medical technology involves nanogenes, just like the ones in Jack’s stolen ship. The horrified Jack finally realises that the cylinder wasn’t empty after all; its contents were just too small for him to see. When the cylinder crashed, the nanogenes got out, and tried to fulfil their programming by healing the injured. But they’d never encountered human beings before, and the first human being they found was the dead Jamie. It was easy enough for them to restore him to life, but they didn’t know what a human being was supposed to look like; thus, they assumed that his internal injuries were normal physiognomy and that the gas mask was a natural part of his face. Now they’re trying to fix everyone who doesn’t match their template of what a human being is supposed to look like -- and nothing will stop them until they’ve transformed the entire human race into gas-masked zombies looking for the child’s mother.

Nancy is the first to see the zombies advancing on the crash site, and the Doctor explains that the cylinder is calling them here to protect itself, believing that it’s under attack. This is a military ambulance, and the nanogenes don’t just heal people, they get them ready to fight on the front lines again. This is why Jamie now has superhuman strength and can speak through radios and telephone lines; he may just be a frightened little boy, but he’s a fully equipped Chula warrior, ready -- and able -- to tear apart the world in order to find his mother. The others are trapped in the crash site by Jamie’s army of zombies, and any second now, a bomb is due to drop and obliterate the cylinder. And since Jack reactivated his ship’s nav-com to get here, the security protocols are active again, and he won’t have time to bypass them -- which means he can only transport himself to safety. The Doctor tells him to do what he has to, and despite Rose’s protests, Jack teleports away, leaving the others behind.

Nancy has broken out in tears, insisting that this is all her fault, but as the Doctor tries to console her, he realises what she means. Nancy is older than she looks, old enough to have given birth four years ago. And since the 1940s aren’t a very welcoming era for a teenage single mother, she lied to everyone, including Jamie, about their relationship. Jamie now pushes open the gates, snapping the padlock without effort, and calling out for his mummy. The Doctor warns Nancy that he’ll never stop looking, and tells her to go to her son and tell him the truth. Tear-stricken, Nancy does so, telling Jamie that she’s his mummy and always will be. As she holds him in a sorrowful hug, a cloud of glowing nanogenes surrounds them both, but the Doctor stops Rose from interfering; the nanogenes are analysing Nancy’s DNA and learning from their mistakes. The cloud vanishes, and the Doctor rushes forward... and removes Jamie’s gas-mask, revealing that he’s now perfectly healthy. Nancy is Jamie’s mother, and thus she shares the same DNA -- and the nanogenes recognised the superior information. Nancy effectively reprogrammed them to understand what healthy human beings are supposed to be like.

The German bomb then drops on the crash site, but at the last moment, Jack’s ship swoops in and catches the bomb in its tractor beam, just as the Doctor had predicted. The bomb is about to detonate, but Jack is holding the bomb in stasis; however, the Doctor tells him that it’s not necessary any more and asks him to dispose of it safely. Jack departs, complimenting Rose on her T-shirt and bidding her goodbye. The Doctor then draws the nanogenes towards himself, ensures that they’ve all got the “software upgrade,” and flings them towards the crowd of zombies -- and within seconds, they’re all perfectly healthy, if somewhat confused, human beings. The Doctor is ecstatic; just this once, everyone lives. He helps the confused Dr Constantine to his feet and advises him to take credit for helping his patients; however, Constantine is rather taken aback when he’s confronted by the elderly Mrs Harcourt, whose missing leg has grown back.

The Doctor sends the confused soldiers and patients to safety and programmes the cylinder to self-destruct, ensuring that there is an explosion at the crash site just as history dictates. The nanogenes will clean up the mess they made and then switch themselves off, and Dr Constantine will help Nancy and Jamie. All is resolved... except for the fact that Captain Jack is hurtling through space with an active bomb in his ship. The stasis field is decaying, any attempt to jettison the bomb will cause it to explode, and there are no escape pods on board; in short, Jack is doomed to die in two minutes. Jack, resigned, orders his ship’s computer to initiate emergency protocol 417 -- his last drink, a martini with, as it turns out, too much vermouth. As he drinks his martini and reminisces about the last time he was sentenced to death, the sounds of Glenn Miller drift through his ship... from the open door of the TARDIS, which has materialised on board. The Doctor and Rose invite Jack inside and advise him to close the door before his ship explodes. Jack does so, and watches, amused, as the Doctor sets the TARDIS in flight and dances with Rose in front of the TARDIS console.