The Doctor takes Rose back home to visit her mother, materialising outside her flats twelve hours after she left. Or so he believes. However, while waiting for Rose to return, a flyer on a nearby telephone pole catches his eye -- a missing-persons flyer with Rose's picture on it. When Rose enters her flat and casually greets her mother, claiming to have spent the night with a friend, the stunned Jackie sweeps her daughter up in a desperate, unbelieving hug -- and, over her shoulder, Rose sees a table covered with missing-persons flyers and posters, all with her name and picture on them. The Doctor bursts into the flat, takes in the situation, and apologetically tells Rose that she hasn't been gone for twelve hours, but for twelve months...
Some time later, outside Jackie's flat, a young boy spray-paints the words "BAD WOLF" on the TARDIS and cycles off. Meanwhile, a policeman sits and listens patiently as Jackie lashes out at Rose for her thoughtlessness in vanishing for over a year without so much as a phone call. Rose claims that she's been travelling, but Jackie angrily points out that she left her passport behind. The Doctor explains that he employed Rose as his companion -- in a non-sexual sense -- but Jackie turns her anger on him, slapping him and accusing him of luring away her daughter for immoral purposes. Rose is embarrassed and remorseful, but despite Jackie's pleas, Rose can't even begin to explain where she's been for the past year.
Later, the Doctor sits with Rose on the roof as she ponders how to deal with having unwittingly traumatised her mother. The Doctor firmly states that Jackie's not coming with them if Rose decides to keep travelling. In passing, he reveals that he's 900 years old, and Rose realises that this is just another of the many things she can't discuss with anyone. As she muses what it's like to be the only person who knows that aliens really are out there, however, an alien spacecraft sputters overhead and careens wildly across the London skyline, belching smoke. As they watch, the ship demolishes Big Ben and crashes into the River Thames. Delighted, the Doctor rushes off to investigate, but the army has cordoned off the crash site and the streets are gridlocked. The Doctor wants to find out what's happening, but he can't get close to the crash site, and he doesn't want to attract the wrong sort of attention by materialising the TARDIS nearby. Rose thus suggests that he watch the news on TV like everyone else.
The Doctor returns to Rose's flat, where Jackie reluctantly lets him in for fear of alienating her daughter further. Jackie's friends and neighbours have joined her to discuss the UFO crash and Rose's return, and the Doctor is having difficulty hearing the television; at one point, he even finds himself fighting for the TV remote with a young boy who wants to watch Blue Peter. Meanwhile, reporter Tom Hitchingson and political commentator Andrew Marr are amongst those reporting the news and its developments. The world is on red alert, flights have been cancelled over North American airspace, and the Secretary-General of the UN has advised people to watch the skies. Divers remove a body from the wreck and take it to Albion Hospital for examination by Dr Sato; there, she reveals her findings to General Asquith, who is startled by the alien pilot's appearance and orders Sato to keep it out of sight until the experts arrive.
There has been no sign of the PM since the state of emergency was declared, and due to the gridlock and the grounding of flights, most of the Cabinet has been stranded outside central London. Thus, Joseph Green -- the rotund MP for Hartley Dale, and Chairman of the Parliamentary Commission on the Monitoring of Sugar Standards in Exported Confectionary -- has unexpectedly become the acting Prime Minister. He seems to be having difficulty handling the pressure, and while junior secretary Indra Ganesh tries to brief him, Green breaks wind, complaining that the nerves are giving him an upset stomach. The equally rotund Margaret Blaine of MI5 and Oliver Charles, Transport Liaison, report that the PM boarded his car that morning, before the emergency, and has since disappeared. Ganesh gives Green a booklet detailing the emergency protocols to be followed in case of alien incursion, and Green takes Margaret and Oliver into the Cabinet office to discuss the situation... but once there, he drops the booklet on the table, and all three begin to giggle like naughty schoolchildren. In all of the confusion, nobody pays any attention to backbencher Harriet Jones, MP for Flydale North, whose afternoon appointment with the PM has been trumped by the ongoing emergency.
Night falls over London, and the Doctor, frustrated by the mundane conversation between Jackie and her neighbours, tells Rose that he's going out for a walk. He assures her that first contact with alien life is something the human race can and must be left to handle on its own, and when she shows concern that the Doctor will leave her behind, he hands her a key to the TARDIS. Mollified, she returns to the flat -- but despite his assurances, the Doctor heads straight to the TARDIS. Upstairs, Mickey Smith emerges from his flat, catches sight of the Doctor, and bolts downstairs to confront him, but arrives just as the TARDIS fades away. Inside, the Doctor struggles to control the TARDIS' flight, even whacking the controls with a small sledgehammer in order to make his ship do what he wants.
Meanwhile, at 10 Downing Street, Harriet tries to convince Ganesh to let her speak with Green, but he refuses to interrupt Green's important meeting for her minor concerns. When Green, Margaret and Oliver emerge from the Cabinet office, Harriet tries to speak with Green, explaining that she's come up with a scheme by which cottage hospitals don't have to be excluded from centres of excellence. Green laughs in her face and walks off with the others. Nettled, Harriet slips into the deserted Cabinet office and drops the report she's prepared in Green's briefcase... but she then notices that he's left the emergency protocols booklet behind, and, curious, she begins to leaf through it.
The TARDIS materialises in a storeroom in Albion Hospital, and the Doctor emerges cautiously -- only to walk straight into a group of soldiers on tea break. The moment of mutual surprise is broken when they hear Dr Sato screaming, and the Doctor instantly takes charge of the situation, leading the soldiers to the morgue to investigate. There, the terrified Sato reveals that the alien came back to life and burst out of its drawer, and the Doctor orders the soldiers to lock down the perimeter and search for the missing alien. However, he then hears movement in the morgue, and investigates to find the alien hiding behind a counter. It looks for all the world like a pig, in a spacesuit, walking on its hind legs. The Doctor tries to approach it, but it bolts, squealing in terror -- and runs straight into a bewildered soldier, who shoots it in the head before the Doctor can stop him. The enraged Doctor insists that the creature was just scared, and watches, mourning, as it dies in front of him. He returns the body to the morgue, where he studies Sato's findings and reveals that the creature is in fact just a pig -- albeit a pig augmented with technology in order to make it look and act more alien. However, Sato points out that the technology used to augment the pig is itself alien, which means that real aliens are responsible for faking a false UFO scare. The Doctor returns to his TARDIS and dematerialises, leaving the confused Dr Sato behind.
Back in 10 Downing Street, Harriet hears voices approaching the Cabinet office and is forced to hide in a nearby closet. General Asquith enters with Green, Margaret and Oliver, berating Green for his appalling lack of leadership; Green isn't returning the White House's calls, he's cancelled the airlift that would have brought senior Cabinet ministers into London, and he hasn't started any of the emergency procedures outlined in the booklet. To Asquith's fury, Green, Margaret and Oliver begin giggling and farting like naughty schoolchildren, and finally Asquith declares that he's using his emergency powers to remove Green from power and place London under martial law. This is a threat that Green takes rather more seriously -- and as Harriet watches in horror from hiding, Green, Margaret and Oliver unzip their foreheads to reveal their true alien forms, and advance on the startled General Asquith.
Mickey enters the Tylers' flat, and is furious to see Rose sitting with the rest of his neighbours. Rose apologises for not visiting him, but that's not nearly good enough; when she disappeared with no explanation, Mickey was nearly charged with her murder. He's been questioned five times in the past year, and even when Jackie blamed him, Mickey couldn't tell her the truth, as he knew she'd never believe him. He now demands that Rose admit the truth; she might as well, because the Doctor's gone without her. Rose refuses to believe this, but when she goes out to see for herself, there is indeed no sign of the TARDIS. She insists that the Doctor wouldn't have left her behind -- and as she speaks, the TARDIS key begins to glow in her hand. Jackie has followed Mickey and her daughter, and although Rose tries to bundle her back to the flat, it's too late. To Jackie's shock, the TARDIS materialises before her eyes.
The Doctor is irritated when Jackie and Mickey walk into the TARDIS behind Rose, and as Mickey angrily accuses the Doctor of ruining his life, Jackie stares about in shock and bolts out of the ship in terror. Rose follows, trying to assure her mother that everything's all right, but Jackie runs back to the flat, and the frustrated Rose returns to the TARDIS to find out what the Doctor has to say. Jackie huddles up in her flat, trying to cope with what she's seen -- and when the emergency alien hotline number reappears on the TV, she calls it up and blurts out her story, claiming that her daughter is in danger because of an alien called the Doctor who travels in a blue box called the TARDIS. These key words trigger an automated alert which Ganesh receives at 10 Downing Street.
Back in the TARDIS, the Doctor -- who insists on calling Mickey "Ricky" rather than admitting he can't remember his name -- explains that the crash landing was faked, but by other aliens. Mickey points out that putting the world on red alert is an odd way to start an invasion... so what are the aliens really up to? The Doctor starts fiddling about with the circuitry beneath the console, but refuses to explain what he's doing, pointing out rather rudely that Mickey doesn't have a hope of understanding it anyway. Rose apologises for the Doctor's behaviour, and assures Mickey that she did miss him, even though she's only been gone for a few days from her perspective. He tells her that he spent the whole year looking for her, and that he never dated anyone else (though, admittedly, most people think he murdered Rose and hid her body somewhere). Now that she's back, she realises that Mickey wants to pick up where they left off -- but before she can decide, the Doctor announces that he's finished his work. He's looped back the TARDIS radar 12 hours to follow the ship's flight path -- and he, Rose and Mickey thus discover that the ship was launched from Earth before crashing back down. The aliens have obviously been here for a while... and what have they been doing for all that time?
"Oliver Charles" has now shed his skin and clothed himself in General Asquith's; however, like the other aliens, he must break wind frequently in order to squeeze himself into the tight disguise. Harriet cowers in the closet as "Asquith" tosses his former skin inside, complaining that he'll now have to give up Oliver's wife, his mistress, and the young farmer he was seeing on the side. As Green, Asquith and Margaret leave, Ganesh rushes up to inform them that their automated surveillance software has detected someone speaking about "the Doctor," who is apparently the ultimate expert in extra-terrestrial affairs. Harriet listens from hiding as Ganesh tells the others that they'll have to enlist the Doctor's help.
The Doctor, Rose and Mickey watch more news footage from inside the TARDIS, and see a group of experts from UNIT, the United Nations Intelligence Taskforce, being escorted into 10 Downing Street. Mickey, who's spent the last year researching the Doctor's past appearances, reveals that the Doctor once worked for UNIT; however, the Doctor decides not to offer his help, as he's changed a lot since the old days and his arrival would just confuse matters. He decides to check out the wreck of the ship instead. However, as soon as he, Rose and Mickey step out of the TARDIS, they find themselves surrounded by police, soldiers and helicopters. Mickey bolts in panic and hides behind the dustbins as the army close in on them, and Jackie protests in vain when her daughter is apparently taken into custody alongside the Doctor. However, they're not being arrested; they're being escorted to 10 Downing Street.
The Doctor admits to Rose that he's visited this planet a lot, and these days, his arrival tends to be noticed. He and Rose arrive at 10 Downing Street, where they wave to the paparazzi and enter the seat of government. Inside, Harriet Jones is trying to mingle with the visiting experts, but before she can speak to any of them, Ganesh arrives and ushers them all out to the briefing room. He gives the Doctor an ID card, but refuses to give one to Rose, who doesn't have sufficient security clearance. Harriet offers to take care of Rose while the Doctor is busy, and escorts Rose out into the hall -- where she breaks down in tears and tells Rose everything that she's seen. Rose accompanies Harriet to the Cabinet office, where they study the abandoned skin suit and try to decide what to do about it. Hoping to find some evidence of alien technology, Rose opens up a nearby closet -- and a body tumbles out. When Ganesh storms in to take Harriet to task for continually getting in the way, he finds Rose and Harriet staring, appalled, at the body of the Prime Minister. Margaret Blaine then strolls into the office behind them and admits to the bewildered Ganesh that she lied about escorting the PM to his car that morning. She then closes the door, unzips her forehead and removes her skin-suit...
Back in her flat, Jackie is being questioned by police commissioner Strickland... a rather rotund and gassy man who seems uncomfortable inside his own skin. Strickland sends the other police away so he can question Jackie alone about the Doctor, and although Jackie insists that she knows nothing about the man, that isn't good enough for Strickland. This Doctor means trouble, and that means anyone associated with him is trouble. And Strickland's job is to deal with trouble. He unzips his forehead and removes his skin-suit...
The Doctor walks into the briefing room, flips through the agenda within seconds and immediately picks out the most important point. Before Asquith can begin the briefing properly, the Doctor speaks up, pointing out that a satellite detected an anomalous blip of radiation beneath the North Sea three days ago, but that the faked crash-landing has distracted attention from it. Worse, it suddenly occurs to the Doctor that everyone who could have investigated the radiation blip is currently in this room. The crash wasn't just a distraction; it was a trap. As he speaks, Green passes wind loudly, and when the Doctor turns on him for the interruption, Asquith unzips his forehead and removes his skin-suit...
The aliens' true forms are now revealed; they are the Slitheen, gigantic, corpulent, baby-faced aliens with extended necks, claws, and elongated arms. In the council estate, the alien that was Strickland advances on the terrified Jackie. In the Cabinet office, the alien that was Margaret Blaine grabs Ganesh by the throat and lifts him up to the ceiling as the horrified Harriet and Rose watch. And in the briefing room, Green activates the charges in the delegates' ID cards, electrocuting every one of the gathered alien experts. The Doctor drops to the ground in agony as the Slitheen burst out laughing...