Martha Jones, a former companion of the Tenth Doctor, calls him to ask for assistance during an investigation by UNIT. Minutes after the Doctor’s craft, the TARDIS, materialises in contemporary Britain, Martha authorises the raid of an ATMOS factory. The Doctor introduces his companion Donna to Martha and UNIT; Donna instantly befriends Martha, but is concerned about UNIT’s ethics.
ATMOS is marketing a satellite navigation system developed by young prodigy Luke Rattigan. The system also reduces carbon dioxide emissions to zero; UNIT requested the Doctor’s help because the technology is not contemporary and might be alien. UNIT are also concerned about fifty-two simultaneous deaths occurring spontaneously several days earlier. Whilst everyone else is studying the technology at the plant, Donna goes through the personnel offices and discovers there are no recorded absences by anyone in the plant: no-one is getting sick.
The Doctor travels to Rattigan’s private school to investigate the system and discovers that the recent events have been plotted by an alien warrior race known as the Sontarans. The Sontarans are part of a battlegroup led by General Staal, “the undefeated”, and Luke is his Earth Asset. Instead of an outright invasion, they are taking control with a combination of human clones, mind control, and ATMOS; Martha is captured by two of the controlled humans and cloned to provide a mole within UNIT.
Meanwhile, Donna returns home to explain to her mother Sylvia and her grandfather Wilfred that she has been travelling with the Doctor, after being advised to do so by Martha. Concerned about the implications of telling the truth, Donna decides against telling her mother. The Doctor investigates the ATMOS device attached to Donna’s car and discovers a secondary function: the device can emit a poisonous gas. Wilfred attempts to take the car off the road, but is trapped when Staal activates all 400 million ATMOS devices installed in cars worldwide.