As the Doctor, Rose Tyler and their new friend Harriet Jones battle the murderous Slitheen in 10 Downing Street, the Doctor realises that the fate of the Earth rests on Mickey Smith. [Edit]

Following from the cliffhanger in "Aliens of London", the Doctor, being extraterrestrial, is able to survive an electrical pulse triggered by the Slitheen Green that has killed the other alien experts in the room; he manages to direct the charge to Asquith, and the shock spreads to Green and the other Slitheen: Margaret Blaine is temporarily stunned, allowing Harriet Jones and Rose Tyler to escape from 10 Downing Street, while Mickey Smith is able to push aside the police inspector that was advancing on Jackie Tyler and pull her from the apartment. The Doctor attempts to get the police, but by the time he has returned, the Slitheen have gotten back into their suits, and the Doctor's claim that the Acting Prime Minister is an alien is rebuffed, with Green instead pinning the deaths of the alien experts on the Doctor, and orders his capture. The Doctor escapes to the upper floors of 10 Downing Street, and helps Rose and Harriet to escape back to the Cabinet Rooms so they can determine what Emergency Protocols are in place for an alien invasion. The Doctor shortly follows them, after learning that the Slitheen are a family, and they are not invading Earth but here for business reasons.

The Emergency Protocols are found to be of no help as they list the alien experts already dead in the room downstairs, and that they cannot launch nuclear weapons at the Slitheen as the codes for the United Kingdom can only be released after authorization by the United Nations, due to a past incident. With no other course of action, they attempt to learn what they can about the Slitheen, and determine they are a calcium-based lifeform from Raxacoricofallapatorius, and that they use compression collars to squeeze their bodies into the human skins, which accounts for their flatulence. The group is called by Mickey and Jackie, having taken refuge in Mickey's flat. The Doctor gives Mickey instructions on how to log into the UNIT website, and uses that to determine that the Slitheen ship is presently in the North Sea, transmitting some signal that Mickey attempts to decode. However, as he works, the Slitheen posing as a police inspector breaks in, but thanks to advice from the Doctor, Jackie is able to douse it with copious amounts of vinegar containing acetic acid, which react with the calcium-based creature, causing it to explode.

At the sense of loss of their brother, Green and the other Slitheen declare a matter of national security and request that the UN release the activation codes to strike against a fictitious mothership that is hanging over London. The Doctor realizes that the Slitheen actually plan to fire the weapons against other countries, starting World War III and leaving the world as a radioactive dump, which they would then sell off to the rest of the galaxy as a fuel source, that fact being advertised through the signal Mickey has decoded. The Doctor recognizes a solution but tells Jackie he cannot promise Rose's safety, but before Jackie can react, Rose tells the Doctor to go ahead, further ordered by the highest elected representative left, Harriet Jones. The Doctor tells Mickey to access the Royal Navy HMS Taurean, a Trafalgar class submarine off the coast of Plymouth, and to fire a Harpoon missile at 10 Downing Street, where all the Slitheen have gathered to try to deal with the Doctor and his group. The area around 10 Downing is cleared while the Doctor, Rose, and Harriet take shelter in the Cabinet Rooms. The Slitheen attempt to escape though are delayed by putting on their human suits as they do not want to reveal themselves to the world at large, and are caught in the explosion when the missile hits. The Doctor, Rose, and Harriet all survive, and the Doctor encourages Harriet to take the position of Prime Minister and help rebuild the government. The entire event is stated in the press as a hoax, and the Doctor has Mickey use a special computer virus to wipe all records of The Doctor from the Internet.

The Doctor cancels the Slitheen advertisement, and declines an offer by Jackie for dinner so she can get to know him better, now that she knows the Doctor is part of Rose's life. The Doctor offers Mickey an opportunity to be part of the crew, but he declines, saying the Doctor's world is not for him. Rose, after packing some her belongings, rejoins the Doctor for more travels. [Edit]