|“||One bullet. One life. The end starts here||”|
—Scorpia Rising tagline
Zeljan Kurst, former leader of SCORPIA, is asked by Yannis Ariston Xenopolos, a Greek billionaire suffering from terminal cancer, to return the Elgin Marbles to Greece. He is promised €40 million, half in advance. MI6 found out about the visit and tried to capture him due to a snitch who was given a change of identity in exchange, but Scorpia agents in the museum (disguised as visitors) help Kurst escape.
He assigns the mission to a new Scorpia member, Abdul-Aziz Al-Rahim, known as Razim for short, who suggests blackmail, attempting to ruin the British reputation with the rest of the world. The plan requires Scorpia to build up a file, codenamed Horseman, on the subject of Alex being used as a spy by the British government for a disgraceful act. The plan is that he will be killed, threatening to expose it, hence ruining the British reputation, unless the Elgin Marbles are returned to Greece.
Razim is studying the issue of pain, with the aim to come up with a measurable unit of pain, naming it after himself, by torturing all kinds of members of society, with a teenager being the top of his wish list, as he explains when exposing a French agent to the same experience.
At a secret prison in Gibraltar, Scorpia manages to free Julius Grief, one of Hugo Grief's clones from Point Blanc who is also Alex's look-alike. Julius is hellbent on revenge over Alex for what he did in Point Blanc. They hide a gun in the prison library for Julius along with instructions, enabling him to get out of the gates by taking his psychiatrist hostage. His death is faked with a remote-controlled car, a duplicate of the one he was driving for escape, which contains a dummy in the front, being sent over a cliff which is released from a barn soon after he drives into it.
Scorpia decides that the best way to start the ball rolling would be for a body leading MI6 to Cairo, where the main action will happen, to be found, and Kurst decides to kill another Scorpia board member Levi Kroll, who opposed the plan initially and is shot in the neck by a sniper. In Britain, MI6 scientists find Kroll's corpse, which was found floating in the River Thames. This causes them to suspect an attack at the Cairo International College of Arts and Education in Cairo, Egypt, where many wealthy children are sent.
At Alex's school, a sniper who is placed on top of a nearby building takes a shot at Alex's classroom. One of the shots hit Tom Harris' (Alex's friend) leg, causing minor injuries. Alex follows the sniper and is able to send the helicopter and the sniper who is escaping in it crashing into the Thames. This gives Alan Blunt a ruse to send Alex on a mission to Cairo to investigate the new head of security Erik Gunter, believing he might have something to do with Scorpia. Unlike in most other missions, Alex's friend and guardian Jack Starbright demands to come along to keep an eye on him, as well as Derek Smithers being sent from MI6 to co-ordinate the mission. Alex is led to a floating market, the House of Gold, where he hears Gunter shooting a weapons dealer, whose body Alex find after he sells him a gun. The market is blown up whilst he is on it. He gets out and survives, but then he is then kidnapped by a mysterious group, who took him to a room where he is waterboarded for information. However, this is quickly stopped by Joe Byrne, revealing that the mysterious group is the CIA, who have recognized Alex as an MI6 spy and believe he is there as an assassin. Byrne explains that they are in Cairo to protect the American Secretary of State, who is planning to make a speech announcing Britain to be less influential as a world power – they are well aware of the furor that will be caused by the speech (mentioning that even the President tried to stop it) and, though unhappy, are forced to provide security. Alex is then sent home, where he then goes to Smithers' house.
Scorpia then begins to target Smithers and kill him. The man booby traps his entire house in Cairo, using gadgets that include itching powder and a doormat which leads to the Cairo sewers. While being chased on the streets, Alex finds out what Smithers' last gadget is - a fat suit which he has been wearing since the moment Alex met him - and discovers that Smithers is in fact a skinny Irishman in his late thirties. He says they should split up, and leaves. Alex gets home, but finds that Jack has been kidnapped and a note that is ordering him to get to a certain location, or she will die. Alex meets at the location, where he gets mugged by Julius Grief and Erik Gunter, and then taken away. Both Alex and Jack are taken to Razim's fort in the Sahara Desert, where Alex is taken to be Razim's next subject. However, for the plan to work out, they cannot physically cause him pain or mark his body in any way. Razim instead decides to use the opportunity to subject him to emotional pain. To do this, he strips Alex down to his boxers, ties him up, and attaches several emotion-recording devices to him. Razim engineers an opportunity to allow Jack to escape from her cell by making sure one of the bars is weak enough to be removed with a knife Jack has stolen earlier, knock out a guard and drive off in an old Land Rover. Unbeknownst to her, the Land Rover has 30 kilograms of explosives connected to it and, with Alex watching live on a screen, Julius detonates the bomb, killing her instantly. Alex's grief is too much for him to handle and he blacks out. Julius starts giggling hysterically, while Razim comments on how more powerful emotional pain is compared to physical.
Alex is bound and gagged, then taken to Cairo, where he is told what will happen by Gunter – when the American Secretary of State decries the United Kingdom and gives her anti-British speech, Julius (posing as Alex) will assassinate her, and in the clamor that follows, Alex's body will be found nearby. This would defy coherent explanation, that Alex killed her. Days later, Scorpia will begin their blackmail, threatening to expose their file on MI6's use of a schoolboy as an assassin unless the Elgin Marbles are returned. As a last request, Alex asks for a cigarette, but as Gunter opens the packet, an irate scorpion Alex hid inside stings him. This immobilizes Gunter enough for Alex to steal his gun and break his nose, killing him when he falls. Alex then rushes inside, just as Julius was sneaking away in order to go to his sniper rifle and kill the Secretary of State. Alex distracts Julius just in the nick of time, so a shot is fired, alerting everyone to the presence of a sniper, with the casualty being a security guard. This organizes the frenzy required, but Julius slips away into the crowd after grabbing the patrol's weapon, leaving Alex to need to give chase or lose him again.
Alex chases Julius through the now raining streets of Cairo, culminating in a grassy verge by the side of a road, where Julius is hit by a car. He claims that Alex wouldn't dare kill him, but as Alex turns away, Julius goes for his gun, and is shot in turn by Alex. He then meets up with the CIA, who are forming a joint task force with the Egyptians in order to take out Razim in the desert. However, they need Alex to come with them to be able to properly locate him, and so as to avoid suspicion when landing. They torture the pilot for the code word so they won't get shot down while approaching the fort, which works out, and Alex poses as Julius when arriving. However, Razim sees through the deception, and a shootout between the Egyptian and Scorpia forces ensues. Alex and Razim then encounter each other on a drawbridge between the two halves of the fort. The bridge fails to support the two and splits. Alex holds on while Razim does not, and he falls into the salt pile below where the man is killed. The fort is neutralized and Operation Horseman is brought down. Later, SCORPIA disintegrates from the pressing embarrassment of being beaten by the same teen three times in a row, and all of the Scorpia members are arrested or executed including Kurst.
Back in England, Blunt is retiring from the scandal in Crocodile Tears and will leave his job to Mrs. Jones. Before Blunt says goodbye, Mrs. Jones reveals that she knows Blunt hired the sniper to fire at Alex's school, which means that he also is responsible for Jack's death. Blunt makes a final message about how she will be faced with the same pressing decision in her career, and how she will have to choose decisions that may kill hundreds in order to save millions.
Alex is adopted by Edward Pleasure, Sabina Pleasure's father, who is confident Alex will get better with his family.
- Despite saying that Scorpia Rising would be Alex's last adventure Anthony Horowitz has since written another novel Never Say Die.