The Doctor uses the TARDIS to take Rose back to her flat, supposedly 12 hours after she left her mother Jackie (in "Rose"), but discovers that they have actually returned 12 months since that point; Jackie declared Rose missing and Mickey Smith was accused but cleared of murdering Rose. As Rose expresses her frustration at the Doctor for not being able to tell the truth of where she's been, a spacecraft speeds through the sky, crashing through Big Ben, and splashes down in the River Thames. Central London is quickly sealed off, forcing the Doctor and Rose to follow events on television. An alien is discovered in the wreckage and taken, under command of General Asquith to nearby Albion Hospital. The general examines the body and asks Dr. Sato, the pathologist, to learn all she can about the creature. As various "alien-welcoming" parties occur in the estate flats that evening, the Doctor sneaks off to his TARDIS alone, promising Rose he will not interfere with Earth's first alien contact and that he won't leave her, and materialises at the hospital. There, managing to influence the guards, he is able to meet Dr. Sato and the alien, and determines that the alien is really just an Earth pig, enhanced by alien technology; someone wanted to fake the alien crash.
Meanwhile, due to the inability to locate the Prime Minister and with gridlock around London, MP Joseph Green, a large, flatulent man and a Chair of a DEFRA committee, is instated as the acting Prime Minister by Indra Ganesh, a Junior Secretary with the Ministry of Defence. Ganesh gives Green the emergency protocols for dealing with an extraterrestrial encounter, and introduces him to Margaret Blaine of MI5 and Oliver Charles, an MP who is a Parliamentary Liaison at the Department of Transport. Ganesh leaves the trio alone, who begin laughing among themselves. Harriet Jones, a backbench MP, attempts to deliver a report to the trio, but ends up overhearing General Asquith complaining to Green of his inactivity. The three think it a joke, passing gas as they laugh, then begin to unzip their heads, revealing a blue light, causing the General to scream. General Asquith is killed, the being occupying Charles now using the General's appearance as its own.
As Rose tries to tell Mickey and Jackie about where she had been for the last year and that the Doctor is her friend, the TARDIS rematerialises back at the flats. The Doctor explains to Rose and Mickey that the alien crash was all faked, and that the ship was actually launched from Earth, meaning that whomever launched it has been on Earth for some time, while Jackie calls the Emergency Alien Hotline to report the Doctor as an alien. Jackie's call triggers a "Code 9" alert; when the Doctor, Rose, and Mickey leave the TARDIS, they are surrounded by soldiers, but while Mickey is able to escape, the Doctor and Rose are escorted to 10 Downing Street. There, they find several other alien experts, including those from the United Nations Intelligence Taskforce, gathered to decide on humanity's course of action. While the Doctor is asked to be a part of the meeting, Rose is not, though Harriet Jones offers to keep an eye on her. Harriet shows Rose the empty skin of Oliver Charles, and on further investigation, they find the dead body of the Prime Minister, which they tell Ganesh about. However, Blaine blocks their exit and begins to unzip her head. Simultaneously, police inspector Strickland who has been talking to Jackie after the Doctor was captured, begins to do the same. In the meeting room, General Asquith also unzips his head, and reveals himself as the alien Slitheen, while Green sends a deadly electrical shock through all the alien experts, including the Doctor. The episodes ends in a cliffhanger into "World War Three".
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