At the Rattigan Academy, students haul reporter Jo Nakashima outside and toss her out with her papers. Their leader, Luke Rattigan, is unimpressed and she gets into her car bearing an ATMOS sticker. Inside the academy, Luke recommends to an unseen ally that Jo be disposed of. Jo is driving to UNIT and trying to call in her story, while following her ATMOS car’s GPS instructions. She ends up on the riverfront and the ATMOS system takes over her car, locks Jo in, and drives into the river.
In the TARDIS, Donna is navigating for the first time and as they pass through the 1980s, the Doctor gets a call from a mobile phone: Martha’s. She asks him to return to Earth and he materializes in an alleyway and meets with her. They embrace and Donna comes out so the Doctor can make introductions. Martha announces that she’s engaged to Dr. Tom Milligan and the two women quickly bond. Martha then gets a call and brings the Doctor and Donna to meet with UNIT troops as they conduct a raid on an ATMOS planet. UNIT suspects alien involvement and brutally arrests all of the factory workers. Rattigan’s secret allies watch by hidden camera and are unimpressed.
Martha introduces the Doctor to Colonel Mace, who is impressed with the Doctor’s record as UNIT’s scientific advisor in the 1970s. Donna is not thrilled with UNIT’s heavy-handed techniques against the factory civilians. Mace explains that 52 people have died of poisoning at the exact same time in 11 different time zones, and all of them drove ATMOS cars. ATMOS is an atmospheric control system that reduces emissions to zero, but UNIT believes the technology is alien.
As the Doctor examines the equipment, two UNIT soldiers, Harris and Gray spot two factory workers who declare an area out of bounds. Upon the orders of their superior, the workers let the UNIT soldiers in. They find an advanced cloning vat with something inside. They call for reinforcements then open it, and a humanoid figure emerges briefly then collapses back into the liquid. A squat armored figure appears and incapacitates Harris, and then dares Gray to fire. It’s rendered their guns and radios useless and incapacitates Gray as well. The factory workers come in and the armored figure orders them to undergo processing, then removes its helmet and announces that it is General Staal of the Tenth Sontaran Battlefield.
The Doctor determines the ATMOS equipment is advanced but not alien. The Doctor is not enthused that Martha is working for the military but she points out that she’s not carrying a gun and is working from the inside. Donna comes back from the factory’s personnel office, having discovered no worker had a sick day. Mace explains that child prodigy Luke Rattigan invented the ATMOS system and now runs a private academy. Donna wonders if she should call her mother about ATMOS and Martha asks if the Noble family knows she’s traveling with the Doctor. Donna admits she left them behind and Martha notes that her own family suffered because of her secrecy.
General Staal sends out the now obedient Harris and Gray and then teleports away. Meanwhile, the Doctor prepares to take a jeep to visit the Rattigan Academy and Donna tells him that she’s going home to talk to her family. The Doctor thinks she’s leaving for good and Donna lets him go on for a while until he realizes he’s wrong.
Martha tries to talk to the factory workers without much luck, and discovers that their heartbeat is higher than usual. Harris and Gray pretend to take her to Mace but escort her to the Sontaran facility in the basement and lock her in once she realizes something is wrong.
Donna returns home and realizes she’s only been gone for a few days, local time. She meets her granddad, Wilfred, who wonders if the Doctor is safe. Donna assures him that the Doctor is, but he suggests she not tell Sylvia. Sylvia comes in and demands to know where Martha has been, but Donna just says she’s been traveling.
The Doctor is driving to Rattigan Academy with Private Ross Jenkins as an escort, and notices that even the military jeeps have ATMOS installed. They meet Luke and look over his science labs, and even the Doctor is impressed. However, he notes that Luke couldn’t have invented the technology on his own, and points out a piece of art that is actually a teleportation device. The Doctor uses it and finds himself in a Sontaran ship in orbit. He teleports back to the Academy and Staal comes after him before the Doctor can disable it. The Doctor challenges his honor and Staal removes his helmet. The Doctor taunts the general and notes they have one weakness, and then bounces a cricket ball off of the wall and into its probic vent on the back of its neck. The Sontaran collapses and the Doctor and Ross escape in their jeep.
Staal fixes the teleporter and beams back to his ship in orbit with Luke, and orders Commander Skorr and his troops to begin the operation. Luke assures them that they have enough units installed to assure success. Skorr then teleports to the basement and confronts Martha, and says they need something more complex than hypnotic conditioning. He activates the cloning vat and a humanoid version of her briefly emerges.
Staal talks to Luke, who mentions the Doctor’s name. The general realizes who they’re dealing with and is pleased that the last Time Lord will die at the hands of the Sontarans. Meanwhile, Skorr renders Martha unconscious and starts to transfer her memories to the clone.
Staal’s men track the Doctor through the ATMOS device in the jeep, and take remote control, driving it toward the window. The Doctor is unable to override but manages to counter the computer’s logic by giving it deliberate counter orders, causing it to deactivate. Staal and Luke conclude that the Doctor is dead once the ATMOS device is destroyed. Skorr confirms that the Martha clone is ready and orders it to go to work.
The Doctor and Ross go to pick up Martha, and Ross goes to requisition a UNIT vehicle without ATMOS. Wilfred comes out and recognizes the Doctor from Christmas Eve. Donna calls to UNIT and the Doctor warns “Martha” about the Sontarans, telling her to brief Moss. The clone tells Moss that everything is normal, while the Doctor tires to remove the ATMOS device from Martha’s car. He ends up activating a hidden device out of time sync that emits gas. Sylvia shows up and recognizes the Doctor from Donna’s wedding, while the Sontarans realize the converter is activated and figure the Doctor is alive. Staal orders his fleet to begin the attack and their ships close in on Earth.
The Doctor realizes the gas is toxic and Donna points out that the converters are in every car in Earth. Wilfred tries to get his car off the street but the Sontarans deadlock every ATMOS car and he can’t get out. All 400 million cars across the Earth begin emitting gas and the Doctor tries to get Wilfred out. Overhead, the Sontarans and Luke begin their war chant as the Doctor looks at the spreading gas in horror.