In a secret meeting room of criminal organization Scorpia, Julia Rothman briefs her colleagues on their latest project, codenamed "Invisible Sword." It is a plan to murder children aged 12 - 14 in Great Britain and destroy the friendly relations between the United States and the United Kingdom. She then later kills one of her colleagues by sneaking venoumous scorpions into his "departing gift" when he speaks of retiring.
Alex Rider is on a trip with his friend Tom Harris in Venice in search of Scorpia, the name that Yassen Gregorovich gave Alex before dying in the prior novel. While investigating at a party being held in the house of Julia Rothman, Alex is captured by a Scorpia assassin called Nile and is left to die in a water room, but manages to escape, barely. Alex is tutored about BASE jumping from Tom's brother Jerry (this is a reference to Tom and Jerry, showing just one reason why Tom is not fond of his parents) and infiltrates the pharmaceutical company Consanto. He runs into Nile again; however, this time Nile takes Alex to see Julia Rothman. Rothman offers Alex a job at Scorpia, which he accepts after Rothman tells him that Scorpia had hired his father John Rider as an assassin. She also tells Alex that John was killed by MI6 during a prisoner exchange at Albert Bridge. Alex's first task is to kill his former MI6 superior, Mrs Jones.
Scorpia sent a letter to the Government informing them of the power of Invisible Sword. To demonstrate, they tell them that they will kill the England B national football team as they arrive at London Heathrow Airport without using any weapons. Despite increased security, the team mysteriously dies. Alex sneaks back into England amid the chaos. He then sneaks into Mrs Jones's apartment to kill her, but is unsuccessful and is arrested.
Alan Blunt, the head of MI6, takes Alex to a COBRA meeting to figure out what Invisible Sword is and how to stop it. With Alex's help, they determine that Scorpia embedded gold-encased nanoshells into the football players' bloodstream. The nanoshells were hidden in vaccinations and contained cyanide, which were activated by satellite dishes, and when they were activated, the gold wore away and the cyanide was released into the bloodstream, killing every single one of the players instantly. Scorpia will then kill London's schoolchildren, including Alex, as they had all recently been vaccinated.
Alex agrees to help MI6 out and pretends to come back to Scorpia. Rothman takes him to an abandoned church; Scorpia planned to put a satellite in a hot air balloon. At a certain height, they will then activate the nanoshells. Alex activates a retainer in his mouth and the SAS invades the church. As the balloon begins to rise, Alex jumps on the balloon and damages the satellites, causing them to plunge to the ground. Rothman is killed by the falling satellite. In the final pages of the novel, Alex learns that his father was a double agent for MI6, and the bridge scene was staged. Scorpia learned that John Rider was still alive and took revenge by blowing up the plane that he and Alex's mother Helen were flying in. In the final scene, as Alex exits the MI6 headquarters, a Scorpia assassin shoots him in the chest. He collapses, sees his parents, and loses consciousness.