400 million cars on Earth equipped with ATMOS devices are suffocating humanity with poisonous gas. Sylvia frees Wilfred from her car by breaking the windscreen. The Tenth Doctor tells Donna’s family to get inside and seal the windows and doors as best they can. He and Donna return to the ATMOS factory, where the Doctor warns UNIT not to engage the Sontarans. The Doctor tells Donna to stay in the TARDIS for her own safety, but the Sontarans locate and teleport the TARDIS aboard their ship.
When the Sontarans prevent UNIT from launching a nuclear missile at their ship with help from the clone of Martha, the Doctor works out that since their ship was safe, the Sontarans were really preventing the disruption of their atmospheric conversion. The Sontarans attack and take over the factory, easily overwhelming UNIT troops. UNIT manages a counterattack and calls in the aircraft carrier Valiant, which puts the Sontarans on the defensive. Following UNIT’s offensive, the Doctor ventures into the factory and discovers the real Martha in one of the Sontarans’ cloning devices. Having long suspected the truth, the Doctor awakens the real Martha, killing the clone in the process. Before dying, the clone reveals the gas is clone feed, which the Doctor deduces is used to breed billions of Sontaran soldiers on Earth. The Doctor tells Martha to keep UNIT from launching any missiles and rushes off.
The Doctor, assisted by Donna, uses the teleport to return the TARDIS to Earth. They teleport with Martha to Rattigan’s institution, finding him distraught over the potential disaster to Earth that he caused. The Doctor constructs his own atmospheric converter, which ignites the poison gas across the globe and allows the humans to breathe. The Doctor is aware the Sontarans will not concede defeat but feels that he needs to give them a chance to withdraw. He teleports to the Sontaran ship and offers Staal the chance to retreat, but Staal calls the Doctor’s bluff and encourages him to destroy them. Humbled, Rattigan reactivates the teleport and switches places with the Doctor, sacrificing himself to activate the device and destroy the Sontarans.
Afterward, Martha says goodbye to Donna and the Doctor inside the TARDIS and prepares to head home. Before she can leave however, the TARDIS doors suddenly snap shut and it dematerialises and heads to another destination.