The book opens with a flashback to 1886 Prague. Bartimaeus, a demon known as a djinn, is enslaved to a Czech magician, who has ordered him to prepare for the imminent attack by the British. The enemy is lead by Gladstone, a magician who wields a powerful staff. The British manage to take the city and kill Bartimaeus' master, releasing the djinn from his magical bond to the magician.
In modern-day London, 14-year-old Nathaniel, a magician professionally known as John Mandrake, has risen in the British government since returning a rare magical amulet. Magicians run the government. He is the assistant of Mr. Tallow, the head of Internal Affairs, an apprentice to Ms. Whitwell, the Security Minister, and even Mr. Devereaux, the Prime Minister, is following the teen's magical career. Because of Nathaniel's magical prowess, Mr. Tallow instructs him to hunt down and stop the rebel group known as the Resistance. The group is made up of commoners — nonmagical people who oppose the magicians' rule. They are known for stealing magical artifacts and vandalizing government buildings.
Kitty Jones, a 16-year-old Resistance member, attends the theater with fellow rebels Fred and Stanley. During the performance, she remembers why she hates the magicians. Three years earlier, Kitty and her friend Jakob Hyrnek had been playing cricket at the park when Kitty accidentally batted a ball that hit Mr. Tallow's car. The magician sent his demon to attack the children, and Kitty was knocked unconscious.
Before Kitty can finish this memory, it is intermission, and she and her companions must fulfill their mission. Kitty and the rebels break into a nearby shop that caters specifically to magicians. They steal money and magical objects, and then against Kitty's orders, Fred starts a fire to burn down the shop.
On the eve of Founder's Day, the holiday to celebrate Gladstone, a row of shops in Piccadilly is destroyed. In the morning, Mr. Tallow and Nathaniel are called to the scene. Mr. Tallow believes the Resistance is behind the attack and therefore lets the matter fall to Nathaniel. The young magician is summoned by the Prime Minister to give a progress report. Nathaniel doesn't believe the Resistance is responsible, but he isn't sure who is to blame. He shares his plan to send out high-level demons to patrol London and wait for the culprit to strike again. The Prime Minister supports his decision.
To help him with the case, Nathaniel summons Bartimaeus. It's been two years since he summoned the djinn. On their previous adventure, Bartimaeus learned Nathaniel's birth name, so he holds power over the magician. Because of this, he can strike a deal with Nathaniel. For six weeks, Bartimaeus will serve and protect Nathaniel without revealing his true name, and when the time is up, Nathaniel will release the djinn.
On the morning of Founders Day, Kitty meets with other Resistance members in a small shop owned by their leader, Mr. Pennyfeather. They learn that the magicians are blaming the incident in Piccadilly on the Resistance. While she and her fellow rebels are sorting through their stolen goods, they learn that Mr. Pennyfeather will give them details of a new job within the week. The conversation with her fellow rebels causes her to remember the attack in the park three years prior.
After being found unconscious in the park, Kitty and Jakob were transported to the hospital. Kitty wasn't injured, but Jakob was permanently disfigured. Because Mr. Tallow claimed he used magic in self-defense, the case went to court. Kitty pleaded her case even though Jakob's family and her parents protested her decision. In court, Mr. Tallow convinced the judge to rule in his favor, and Kitty was required to pay a 600-pound fine. After Kitty fled the courtroom, a man followed her and introduced himself as Mr. Pennyfeather. He told her that he had heard her story in court and was willing to pay her fine if she called him during the following week.
Back in the present, Bartimaeus and many other demons are placed around London and instructed to watch for another attack. On the fourth night, Bartimaeus hears a commotion and follows it to the British Museum. After he transforms into a Minotaur and enters the museum, he discovers a cloud of darkness that his magical sight cannot penetrate. A stone hand grabs him, and the touch alone is almost enough to kill the djinn. Bartimaeus manages to get away from the creature by turning into a cat, but before he can escape the building, it collapses on him.
After the creature leaves, Bartimaeus is discovered inside the remains of the museum, and the djinn is revived. He tells Nathaniel and the other magicians assembled that the creature was a golem, a giant man-shaped monster made of clay. Golems are invincible to attack. The magicians doubt Bartimaeus, as golems haven't been seen in hundreds of years.
Upon further investigation, Nathaniel discovers that the golem's eye, one of the two artifacts needed to summon a golem, was stolen from the Artifacts Vault. Ms. Whitwell instructs Nathaniel to go to Prague to learn more about the golem and the second artifact, an ancient spell known by the Czechs.
Meanwhile, Kitty thinks back to the days after her trial. When she visited Jakob's home, he told her she was foolish to go to court. He also told her that his famous bookmaker family was planning to take revenge on the magicians by altering some of the text in books. Before she left Jakob's house, his grandmother gave Kitty a silver pendant.
Later, Kitty contacted Mr. Pennyfeather, and they made plans to meet at a coffee shop. On her way to the meeting, Kitty was attacked by a demon, but she destroyed it and continued to the coffee shop. Mr. Pennyfeather revealed that the attack was carried out by one of his men to test whether Kitty had a resilience to magic, as he suspected. He told her that a magician killed his wife and that had spurred him to seek revenge. At that point, Kitty joined the Resistance and learned that all of its members are impervious to magic.
Back in the present, Mr. Pennyfeather reveals that the big job he's been researching is breaking into Westminster Abbey. All the famous and powerful magicians are buried there. He intends to break into Gladstone's tomb.
Nathaniel and Bartimaeus travel to Prague where they meet with a British spy named Harlequin. The spy tells Nathaniel that the Czechs have a collection of golem eyes, one of which went missing, and they may still know the spell to bring a golem to life. Harlequin needs to make further inquires about the spell, so they agree to meet in the Old Town Square the next day.
Back in London, Kitty is sent to meet a mysterious magician who has agreed to help the Resistance in exchange for Gladstone's cloak and staff. The magician gives her the key to Gladstone's tomb and a bag containing what the group needs to make it through the hex protecting the tomb. The man also arranges a way for the group to enter the abbey. He never reveals his identity during the meeting. The night of the raid, all is as the magician says, and the group makes it into the abbey, past the hex and into the tomb.
Entering the tomb, the group finds it empty except for Gladstone's sarcophagus. While the men try to open it, Kitty explores the room and falls through a wall at the back of the room. Behind the magical wall are skeletons. When she reveals her discovery to the others, they seem unconcerned. After they open the sarcophagus and begin looting it, they are surprised by a demon named Honorius, who has taken residence in Gladstone's bones. The demon kills every Resistance member there except Nick and Kitty, who manage to escape with Gladstone's staff.
In Prague, Nathaniel buys a hotdog from the stand where he and Harlequin decided to meet. Before Harlequin shows, the police arrive and kill the man running the hotdog stand. After Bartimaeus and Nathaniel evade the authorities, Nathaniel finds a card in his hotdog and realizes that Harlequin was running the stand as a disguise.
The card gives them the name and address of their next contact. They find their contact, Mr. Kavka, in the middle of writing the spell to summon another golem. Upon questioning, he reveals that he's being blackmailed into completing the spell. If he doesn't do it, his family will be killed. A man arrives, and Nathaniel recognizes him as an assassin he faced in the past. During a fight, the assassin and Kavka die, and the spell is destroyed.
When Nathaniel returns to England, his presence is requested at Westminster where the Resistance has struck. Nathaniel learns that Honorius, the demon Gladstone used to protect his tomb, has encased itself in the magician's remains and is running about London. To stop Honorius, the magicians send their demons to scour London. Bartimaeus finds the skeleton and manages to throw it in the Thames.
Nathaniel also learns that two commoners escaped the tomb, one with Gladstone's staff. With the bodies of Resistance members found in the tomb, the incident is blamed on Nathaniel who was in charge of bringing down the Resistance. Because of this, the Prime Minister gives the case to Police Chief Duvall and his army of werewolf officers, the Night Police. Despite being off the case, Nathaniel investigates the incident. He links Kitty Jones to the Resistance and believes she has the staff.
Kitty is still evading the magicians and hides Gladstone's staff in a Resistance weapons cellar. Relieved of her burden, she returns to her parents' home. Nathaniel is waiting for her and tries to arrest her, but she fights back. After Nathaniel summons a demon, Kitty destroys it, leaving the magician and her parents stunned.
Bartimaeus returns to Nathaniel with news of Honorius' demise. That night, Mr. Makepeace, a close adviser to the Prime Minister, visits Nathaniel. Makepeace is concerned that Duvall, the Police Chief, is trying to get Gladstone's staff so he can overthrow the Prime Minister. Makepeace offers to help Nathaniel get the staff from Kitty so the weapon won't fall into the wrong hands. With Makepeace's help, Nathaniel learns about Kitty's connection to Jakob Hyrnek. He sends Bartimaeus to kidnap Jakob so they can trade him for the staff.
Kitty learns about the kidnapping, but on her way to the house where Nathaniel is holding Jakob, she encounters the Night Police. Nathaniel witnesses her turmoil and sends Bartimaeus to save Kitty. Bartimaeus is successful, but the police arrest Nathaniel and Jakob for treason before they can meet up with Bartimaeus and Kitty. While they wait for Nathaniel, Kitty and Bartimaeus commiserate over their mutual dislike of the magicians. The djinn tells Kitty that throughout history the magicians have been brought down by commoners with resilience to magic. He tells Kitty how to destroy a golem. She would need to remove the spell written on parchment in the golem's mouth.
Nathaniel is brought before the Prime Minister and discovers that the police have been following him. His private investigations and strange activities point to his involvement with the Resistance. Because of his loyalty in the past, the Prime Minister allows Nathaniel the opportunity to retrieve the staff and prove himself. When Nathaniel takes Jakob to meet Kitty and trade for the staff, he promises to allow them one day to disappear after they give him the staff. With this in mind, Kitty leads them to the weapons cellar and hands over the staff.
Once Nathaniel has the weapon, he breaks his promise. Kitty manages to distract Bartimaeus and Nathaniel while she and Jakob try to escape in Nathaniel's car. When she reaches the vehicle, Honorius jumps out. The demon had survived, even though Bartimaeus threw Gladstone's skeleton in the Thames.
Honorius declares his intention to kill Kitty and Bartimaeus and retrieve the staff, but before he can, the golem appears. After Honorius tries to fight the golem and is killed, Nathaniel attempts to use Gladstone's staff to destroy the golem. He is knocked unconscious because the staff's power rebounds. Kitty and Jakob now have the chance to escape, but Kitty stays. Using her resilience to magic, she is able to retrieve the spell from the golem's mouth. Only then do they quickly escape. When Nathaniel wakes, Bartimaeus tells him that the golem killed Kitty and Jakob.
Now that the spell is removed from the golem, its last act is to return to its master. To discover its master, Nathaniel and Bartimaeus follow the golem. It marches through London. It travels to the hall where the government ministers are meeting and falls apart at the Police Chief's feet, indicating Duvall as a traitor. With staff in hand and proof that there was a golem, Nathaniel's good name is restored.
Nathaniel is promoted to head of Internal Affairs and quickly falls into the lavish life of a well-to-do magician. Bartimaeus tells him that he's completely lost all of the goodness of the boy Nathaniel and is now completely John Mandrake, a selfish, corrupt magician. Nathaniel dismisses Bartimaeus.
Jakob's family forges passports for Jakob and Kitty so they can travel to Brugges, where Jakob has family and the magicians don't have complete control of the government. But because of her resilience to magic, Kitty decides to remain in London so she can help the Resistance when the time comes.