The book begins with Alex Rider learning that his uncle and adopted parent, Ian Rider, has been killed in a car crash. Unknown to Alex and his housekeeper, Jack Starbright, Ian's job as a banker was actually a front for his role as an MI6 agent. Alex becomes suspicious upon being told that Ian had been not wearing his seat belt and discovering that Ian's office has been emptied out. He finds his uncle's car at a wrecking yard, and discovers that his uncle had been murdered. After a near escape from a car crusher, Alex is asked to visit Ian's former employers, a bank called "Royal&General." He breaks into Ian's office, discovering evidence of his uncle's double life before he is knocked out.
After waking up, Alex meets MI6 head Alan Blunt and his deputy, Tulip Jones. They reveal the truth about his uncle's job, and explain that they had sent Ian to investigate Herod Sayle, a wealthy Lebanese businessman who has developed a revolutionary new computer, the Stormbreaker. Sayle plans to give a free Stormbreaker to every secondary school in the United Kingdom, accompanied by a grand activation ceremony in the Science Museum, supposedly as a gesture of thanks for the country taking him in when he was a child. In his last communication with them, Ian had warned MI6 that the Stormbreakers could not be allowed to leave Sayle's manufacturing plant, but before he could explain, he was assassinated by Yassen Gregorovich, a professional killer supposedly working for Sayle, on the return to London.
Intending to use him to covertly investigate Sayle, MI6 recruits Alex by essentially blackmailing him; if he does not cooperate, Jack will be deported back to America, his house will be sold and he will leave his school and friends for an academy until he is of age. They put him through a grueling SAS training camp, before deploying him to Herod Sayle's base in Cornwall, using the alias of another boy, Felix Lester, who won a competition to visit the plant and be the first child to use a Stormbreaker. To aid him in his mission, Alex is given a grappling hook disguised as a yo-yo, acne cream, and a Game Boy Color which functions as a transmitter, smoke screen and bug detector, by MI6 agent Smithers.
Sayle shows Alex around his mansion, which houses a large jellyfish aquarium containing a large Portuguese Man o' War. Alex also meets Mr. Grin, a henchman whose name derives from his time as a circus performer, catching knives with his teeth. An accident left him without a tongue and two large scars which give him the appearance of constant smiling.
Initially the trip goes well, with Alex finding a cryptic diagram made by his Uncle Ian in the canopy of his bed. However, Sayle grows to dislike Alex, after Alex is discovered in a restricted area of the base, and later defeats Sayle in a game of snooker. While investigating the base at night, Alex sees several of Sayle's agents unloading metal cases with great care from a nuclear submarine, with Yassen supervising. When one of the agents drops a metal case, he is promptly shot dead by Yassen. The next afternoon, Alex decides to head to the local library to do further investigations, but finds himself attacked by a pair of armed guards on quad bikes. He survives by tricking the guards into crashing: one collides with an electric fence while the other falls from a cliff face.
While searching the library, Alex finds a map in a book about tin mining which matches the diagram left by Ian. He also learns that Ian had borrowed several books about viruses, and assumes that Sayle plans to use the Stormbreaker network to release a computer virus. Alex investigates the mine and, following the path left by his uncle, discovers a large computer manufacturing facility, where the Stormbreaker computers are being filled with a strange fluid. Alex realizes that the 'viruses' being investigated by Ian were not computer viruses, but biological weapons. Alex is detected, and nearly escapes but is eventually caught and tranquilized. When he comes to, Herod explains to Alex his plan.
When Sayle attended school, he was bullied because of his accent and skin color. The worst bully was none other than the future Prime Minister, leading him to despise English children. As a result, Sayle plans to take revenge on the Prime Minister and Britain with his "April Fools Joke"; when the computers are activated by the Prime Minister, the virus, a potent strain of smallpox, will be released into every school in the country, killing every schoolchild and teacher in England as well as those in Scotland, Wales and Northern Ireland.
Alex is then left handcuffed to a chair, until Nadia Vole, an assistant of Sayle's, frees him, claiming that she is a fellow spy who worked with Ian Rider. However, as they head to find a mobile phone to call MI6 and inform them of Sayle's plan, she triggers a trapdoor which drops Alex into the jellyfish tank and stays behind to watch him die. Alex eventually gets free by using the acne cream gadget to damage the tank's supporting iron girders, causing it to rupture and sending thousands of gallons of water crashing into the room. Unfortunately for Vole, she was directly in front of the tank when it burst, releasing the immense jellyfish and causing it to land right on her, killing her painfully and instantly. Snatching up a harpoon gun, Alex rushes outside to find that Sayle's private helicopter has already left, leaving only a cargo plane on the tarmac. Using the handle of the harpoon gun, Alex knocks out a guard, taking his jeep and pistol. As he starts the jeep, several other jeeps start to pursue him as the cargo plane starts to take off. Through some fancy driving and good fortune, Alex manages to cause the destruction of the hostile jeeps. Tying the nylon cord of the yo-yo gadget to the harpoon with the yo-yo clipped to his belt, Alex shoots the harpoon which catches on the underbelly of the airborne plane. Using the gadget, he gets himself on to the plane where he confronts the pilot, who is none other than Mr. Grin. Alex instructs Mr. Grin to fly to London by threatening him with the pistol.
When they are finally over London, Alex realizes that there is not much time left before noon. He spots several parachutes and uses one to jump off the plane. Mr. Grin turns the plane around hoping to ram into Alex. Alex pulls out the Game Boy Color and activates a cartridge disguised as a game called "Bomber Boy", which activates a smoke bomb. Unable to see, Mr. Grin loses control of the plane and fatally crashes into a dock near the River Thames. Alex crashes through the roof of the Science Museum and dangles from his parachute which had gotten caught on a beam. Alex draws the gun he took from a guard back at Sayle's mansion and fires blindly at the Stormbreaker computer, one accidentally hitting the Prime Minister and Sayle himself being struck by two more, though he inexplicably vanishes. Mrs. Jones saves Alex's life by ordering security not to open fire on him. MI6 immediately recalls all the computers, citing "safety issues".
Later, after a debriefing by Alan Blunt and Mrs. Jones, Alex enters a taxi. The driver is in fact Sayle who holds Alex at gunpoint. He leads Alex to the top of a building where he is about to shoot Alex, but is himself shot by Yassen Gregorovich, who lands in a helicopter. When Alex questions Yassen about why he shot Sayle, Yassen explains that Sayle had become an embarrassment to the people he (Yassen) worked for, so he had to be eliminated. Knowing that he is facing his uncle's killer, Alex tells Yassen he will one day kill him, but Yassen brushes aside the comment and tells Alex to drop the spy business and become a normal schoolboy again, before leaving in the helicopter.
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