The episode opens with a tour bus being taken around the new Atomic Station in Australia that is reclaiming the desert by using atomic irrigation to pump millions of gallons of sea water into the desert to be used for agriculture. The reporters are not convinced of the safety of the project due to the risk of a nuclear explosion. Meanwhile the Hood is trying to discover the secret of the plant but is caught by security. In the ensuing gunfight, the Hood accidentally hits a gas pump and it explodes. The fire rapidly spreads through the station and soon the staff have to evacuate. The only thing that could have saved them would be to cut off the seawater intake. The plant explodes and sends a radioactive cloud towards Melbourne. But about a week later the wind pushes the cloud back into the desert.12 months later, a European professor has invited a group of army representatives to show off his new invention: the Mighty Atom. It is a very powerful camera concealed in a robotic mouse that takes photos of control panels by recognizing the profiles of people who use them. After a brief demonstration, one of the representatives is revealed to be the Hood in disguise who hypnotizes everyone and steals the invention.
He immediately visits a new Atomic Station in the Sahara desert that is just beginning operations. Using the Mighty Atom, he takes photographs of the station's control room. After he completes his mission, he gets the idea to repeat the accident that destroyed the Australian plant last year in order to lure out International Rescue and steal their secrets, too. He plants bombs around the plant and they explode, causing a fire that rapidly spreads. In the control booth, the controller realises that sabotage is afoot and calls International Rescue. Thunderbirds 1 and 2 take off with Thunderbird 4 and Lady Penelope, who has been desperately waiting to go out on a rescue mission. Virgil drops Thunderbird 4 and Gordon near the seawater intake of the plant. When they land at the plant, the Hood sends the Mighty Atom into Thunderbird 2 with Penelope still inside. Meanwhile, Scott and Virgil push in the control rods to stop the reactor and Gordon destroys the water intake, saving the plant from another atomic disaster.
The Hood returns to his temple hideout convinced that the Mighty Atom has taken the information he requires. However, he finds only pictures of Lady Penelope screaming at what she supposes to be a regular mouse. In his rage, the Hood pounds the Mighty Atom into pieces.