While on holiday in the South of France with his friend Sabina Pleasure, Alex Rider runs into the assassin Yassen Gregorovich, who killed Alex's uncle in the first novel Stormbreaker. When the Pleasures' holiday home explodes in a supposed gas leak, Alex suspects Yassen is involved and sneaks onto his yacht. Yassen captures him and enters him in a bullfight as punishment. After escaping, Alex calls a number he found on Yassen's mobile phone and hears pop star Damian Cray's voice. He tells MI6 about this, but Alan Blunt refuses to follow up on it as he believes it would be politically unwise if the press ever found out that MI6 was investigating Cray. Alex tells Sabina about his double life as a spy, but she does not believe him and refuses to speak with him.
Alex meets a photographer named Marc Antonio in Paris; he reveals that Sabina's father was investigating Cray, and Antonio is killed shortly afterwards by an assassin. Alex goes to Cray Industries in amsterdam, where he hears Yassen and Cray conversing about a flash drive. Cray catches Alex as he tries to sneak away and puts him in a real-life version of Feathered Serpent, a new video game developed by Cray Software Industries (the game was just a cover for getting a huge factory to develop a flash drive). Alex escapes and steals Cray's flash drive. In response, Cray kidnaps Sabina and holds her for ransom. Alex attempts to force Cray to release Sabina, but Cray outmaneuvers him and forces Alex to hand over the flash drive.
Cray reveals his plan, code-named "Eagle Strike": he will board Air Force One and use its missile room to launch nuclear missiles at major drug-running countries to eradicate the drug trade. After creating a diversion using a plane full of fake nerve gas, he, Yassen, Alex, and Sabina sneak aboard Air Force One at Heathrow Airport. Cray plugs in the flash drive and activates the missiles. He then orders Yassen to kill Alex and Sabina; upon Yassen's refusal, Cray shoots Yassen and then Alex. Alex, saved by a bulletproof jersey (given to him by Mr. Smithers), gets up and pushes Cray out of the plane, along with a food service cart. He is then sucked into the engine and shredded to pieces. The food cart getting sucked into the engine results in the engine's destruction, causing the plane to lose control. Cray's pilot Henryk attempts to abort the plane take-off, but, as the plane has already reached V1 speed, he cannot do so safely and crashes the plane off the runway, breaking his neck in the process. Alex and Sabina survive the crash and Sabina presses a self-destruct button to destroy the missiles.
As he lays dying, Yassen tells Alex that Alex's father, John Rider, worked with him as an assassin and that if he does not believe him, to go to Venice and find something called "Scorpia", which is later revealed in the subsequent novel as an evil intelligence company. Alex is stunned at this revelation. At the end of the novel, Sabina tells Alex that she will be moving to San Francisco and then they share a kiss underneath a bridge.