The TARDIS lands at Powell Estate where Rose lives. The Doctor explains that, local time, she's been gone about 12 hours, and Rose goes to see her mother, Jackie, while the Doctor looks around. He notices a "missing person" leaflet with Rose's picture on it and runs upstairs. Upstairs, Rose finds her mother, who is shocked to see her. She hugs her daughter and Rose sees all the missing posters that say she's been missing for a year. The Doctor comes in and tells her what's happened, and an angry Rose demands an answer. Rose claims she was traveling, but Jackie points out she left her passport behind and doesn't believe her lies. Jackie wonders why she can't say but Rose refuse to speak about it.
Up on the roof, Rose and the Doctor discuss the situation and she wonders what to do. A giant alien spacecraft passes overhead at that moment, billowing smoke, and flies over London. It crashes through Big Ben and comes down in the Thames. As the Doctor and Rose run to investigate, they discover that the streets are tied up in traffic and the military is mobilizing to contain the panic. The Doctor thinks it's safer not to use the TARDIS, so they go back to the Tyler flat and watch the news with the neighbors. The world rallies and the government prepares, and divers find an alien body in the wreckage. It's taken to Albion Hospital and the burly General Asquith arrives to lead the investigation.
At Albion Hospital, Asquith meets with the doctor, Dr. Sato, and they examine the body. Sato confirms that it's a real body and Asquith tells her to hide the body until the government experts arrive. As he leaves, Sato asks the general if the rumors about the Prime Minister are true, and Asquith chooses not to answer.
The news anchors are reporting that the Prime Minister hasn't been seen since the emergency began. Joseph Green, the Chairman of Sugar Standards, arrives at Downing Street. Inside, he's greeted by an aide, Indra Ganesh, and a small-town MP, Harriet Jones, informs them she has an appointment with the Prime Minister. Oliver informs her that they're otherwise occupied with the emergency and brushes her off. As they go upstairs, the nervous Green is informed he's the acting Prime Minister. As he nervously flatulates, he demands to know where the Prime Minister is. Ganesh admits that no one knows and the PM has disappeared. Upstairs, Ganesh takes Green to meet with Oliver Charles, the transport liaison, and Margaret Blaine, the head of MI5. Blaine has no news on the PM's whereabouts and Oliver has no record of the car the PM was using. Green goes into conference with Oliver and Margaret, after Ganesh gives him the government protocols for dealing with alien invasion. Once alone, the three officials laugh triumphantly as they look at the protocol case.
That night, the Doctor slips out of the flat and Rose goes after him. He admits he's bored with the human conversation, and figures the ship was an actual crash and it's none of his business and Mankind will have to handle first contact on their own. When Rose wonders if he's going to leave on her, he gives her a TARDIS key to reassure and goes off for a wander. Many of the people on the street are celebrating their encounter with aliens. As the Doctor goes to the TARDIS, Mickey spots him and runs down. Meanwhile, the Doctor dematerializes the TARDIS and pilots it to Albion Hospital, leaving before Mickey can catch him.
At 10 Downing Street, Harriet brings Ganesha a cup of coffee but he refuses to let her in. When Green, Oliver, and Margaret come out, she asks Green to submit her paper. He tells her to get some perspective and leaves with the others. When they leave and Ganesha follows, Harriet goes into the conference room and closes the door, and puts it in the case with the emergency protocols. When she notices the file name, Harriet reads it.
As the hospital, Sato is working when she hears a noise coming from the cabinet where she placed the alien. In the basement, the Doctor leaves the TARDIS and starts exploring. He walks into a room full of soldiers who immediately draw their guns and capture hm.
Sato approaches the cabinet door and the door bursts open. The Doctor hears her scream and leads the soldiers to investigate. They find the injured Sato and she tells them the alien is still alive. Taking command, the Doctor tells the soldiers to spread out and search the hospital. He starts searching and finds the alien in the next room. He tries to communicate with the short pig-like creature but it runs off, screaming. It charges toward the other soldiers, who shoot it down before the Doctor can intervene. He comforts it as best he can but there's nothing he can do to save it.
When Green and the others return with Asquith, Harriet hastily puts the emergency protocol file back and hides in a closet. Asquith demands answers from Green, who doesn't seem to take the crisis seriously. He laughs along with Margaret and Oliver, and they all fart continually. When Asquith demands to know where the rest of the Cabinet is, Green informs him that he didn't bother to fly the others in. When Asquith declares martial law, Green opens the top of his skull and a blue light radiates out. Margaret and Charles do likewise, as Harriet secretly watches from the closet. She turns away in horror as Asquith screams.
The Doctor examines the alien and explains to Sato that it's a fake, a mish-mash of stitched together animal parts. However, its brain has been augmented with alien technology. Sato wonders why aliens would create a fake alien, but the Doctor slips away without answering and departs in the TARDIS.
Back at the flat, Mickey arrives and is shocked to discover that Rose is back. He explains that when Rose seemingly disappeared, the police questioned him and Jackie accused him of abducting her or worse. He tells her that the Doctor left in the TARDIS and she storms out, and Mickey goes after her. As Jackie follows them, Mickey figures that the Doctor dumped her. The TARDIS key glows and the TARDIS materializes. Rose tries to get Jackie inside, but she watches as the TARDIS materializes and Rose goes inside. Jackie and Mickey come in and Mickey gets angry, while Jackie runs out. Mickey points out that it's odd that aliens would set off a red alert to begin an invasion, and the Doctor concedes it's a good point.
Inside, Jackie watches the news reports about alien sightings and calls the listed number. She reports the Doctor and the TARDIS by name. The message is flagged at government headquarters.
Rose apologizes to Mickey, who explains that he spent a year searching for the TARDIS. She admits that she missed him and asks if he's seen anyone else, and Mickey says he hasn't. He wonders if she's going to stay and starts to kiss her, but the Doctor interrupts and announces he's traced the path of the spaceship. It shows that it came from Earth in the first place, and the aliens responsible have been there for a while.
Harriet watches as the Charles Oliver creature dons a suit that looks like Asquith, and complains about the compression of the gas exchange. "Asquith" puts the suit in the closet but doesn't notice Harriet hiding in the back. Once they leave, Harriet picks up the skin suit. Meanwhile, Ganesh comes in and tells Asquith that they've found the key word "Doctor." They know him as the ultimate expert on extraterrestrials and Ganesh insists they need him right now.
The Doctor, Rose, and Mickey are watching newscasts on the TARDIS viewscreen when the Doctor spots UNIT arriving at Downing Street. However, he figures that he needs to go in undercover to keep things simpler. However, as he steps out, government helicopters arrive and take the Doctor and Rose into custody, while Mickey runs off and hides. Jackie comes out and tries to get to her daughter, but the soldiers stop her, and the Doctor and Rose surrender.
As they're taken in a limo, the Doctor explains that they're being taken to 10 Downing Street to meet with the government. He admits that he's been noticed and the government want him as an expert on aliens. They arrive and the Doctor waves to the press and then goes inside.
A burly police officer, Strickland, interrogates Jackie at her flat. He apologizes for passing gas and orders the other policemen out.
Harriet slips into the room with the alien experts, while Ganesh gives the Doctor a security badge and explains that Rose doesn't have the necessary clearance to go in. The Doctor reluctantly gives in and Harriet offers to look after her.
The experts gather in the conference room and Green and Asquith greet them.
Harriet confirms that the Doctor knows about aliens, and then breaks into tears.
Asquith calls the meeting to order, but the Doctor interrupts to point out that there was anomalous signals from the North Sea three days ago. The government was about to investigate and then the ship crashed, and the Doctor figures it was a diversion.
Harriet tells Rose what she saw and shows her the skin suit. Rose searches the conference room for technology and finds the dead Prime Minister in a closet. Ganesh comes in and discovers what they've found.
The Doctor suggests that the aliens sets the entire thing up as a trap.
Margaret comes into the conference room.
Jackie tries to explain to Strickland about the TARDIS. He warns that anyone associated with the Doctor is TARDIS, and then unzips the skin suit he's wearing.
Margaret admits she lied about seeing the Prime Minister drive away.
The Doctor figures that the aliens wanted to lure all of the alien experts together and kill them at one time. Asquith removes his skin suit, revealing a green-skinned alien beneath.
Margaret removes her skin suit and reveals a similar alien form.
Jackie turns and sees Strickland in his true form.
The Asquith alien informs the Doctor and the others that they are the Slitheen.
Margaret chokes Ganesh to death.
The Strickland alien advances on Jackie.
Green activates a remote which triggers an electrical charge, electrocuting The doctor and the other alien experts via their security badges.