In The Amulet of Samarkand, Nathaniel starts off as a young boy who, at the age of five, had been given up by his parents to apprenticeship under a mediocre Whitehall magician named Arthur Underwood, the assistant minister of Internal Affairs. Underwood begins teaching the boy in magic, but Nathaniel, being inquisitive, decides to advance his education to higher levels without the knowledge of his tutor.
However, at the age of eleven, in his master's house, Nathaniel is publicly humiliated by a greedy and ambitious young magician named Simon Lovelace. In a fit of juvenile fury, Nathaniel hatches a plan for vengeance. He sets several mites (a weak kind of imp) on Lovelace, but Lovelace is powerful and stops the mites, then proceeds to beat Nathaniel as punishment.
Later, after much research and preparation, Nathaniel summons Bartimaeus, a 5,000-year-old djinni, to exact his revenge on Lovelace. Mrs. Underwood - Nathaniel's master's wife - inadvertently reveals Nathaniel's true name to Bartimaeus. This vastly limits Nathaniel's control over the djinni, because spells can be cast on people when their true name is known (hence the practice of assigning names).
In the end, Nathaniel earns the respect of the majority of the other magicians including Rupert Devereaux, the Prime Minister. He is accepted as a magician in the government.
The second book picks up almost three years later and features Nathaniel as a junior magician working his way up the government ranks. He is described as one of the governments' rising young stars. In this book, Kitty Jones is introduced as an important character. She is a part of the Resistance movement, which seeks to end the oppressive rule of the magicians. Nathaniel is tasked by his superiors to crush the Resistance movement and capture the members. His task is complicated when a seemingly invulnerable clay golem starts to make random attacks on London. Much to the displeasure of Bartimaeus, Nathaniel recalls the djinni to aid him in uncovering the origins of the golem, and to save his own skin.
During the course of the book Nathaniel is almost fired from his post and executed for treason. By the end of the book however he has come back to favor when Duvall's conspiracy comes to light.
In Ptolemy's Gate, Nathaniel has risen to the ruling Council and is arguably the most powerful magician in the government. He stands against a force of hybrid magicians with spirits trapped inside them, led by Nouda. Romantic feelings are hinted at in the book at various points between Kitty and himself. Nathaniel summons Bartimaeus into his body to help fight the Hybrids with Gladstone's staff, and destroys most of them, leaving only Nouda alive. However, during this fight, Nathaniel is seriously injured and he loses strength quickly, even with Bartimaeus' assistance. When Nathaniel and Bartimaeus confront Nouda, Nathaniel dismisses Bartimaeus which saves Baritmaeus just prior to the staff being destroyed killing both Nouda and Nathaniel. Bartimaeus returned to the Other Place, but is known to have survived; according to his "journal", he was summoned by a female magician with a stutter afterwards. Kitty, in the end, goes visit her old friend Jakob before she begins to travel around the world in a new life.