The film opens with a fantasy sequence in which Johnny English (Rowan Atkinson), an inept British Intelligence agent, is "Agent One". He sneaks into a building, distracts two guard dogs with toys, knocks out two guards and seduces a woman who threatens him. He is awakened from his fantasy, just as he is about to kiss the woman, by his sidekick, Angus Bough (Ben Miller). After being assured that English has checked thesubmarine hatch codes personally, the real Agent One (Greg Wise) leaves on a mission. The audience then learn that Agent One died in action when his submarine hatch "failed to open". A bomb then wipes out Britain's remaining agents, all of whom were attending the funeral of Agent One, leaving only English. Nobody notices the hearse, which sped from the scene minutes earlier.
Before his death, Agent One was investigating a plot to steal the Crown Jewels. Together with Bough, English takes over the case. While investigating, English becomes attracted to a mysterious woman, Lorna Campbell (Natalie Imbruglia), whom he meets at the unveiling of the newly restored Crown Jewels, where English is in charge of the security. The power to the room is cut, and English accidentally knocks out the chief of security, before pretending to fight a criminal in another room in an attempt to cover up this fact. Later, Bough and English follow a tunnel and find the Jewels, but fail to stop the thieves after English accidentally ejects the magazine from his pistol. English chases their car, a hearse, but accidentally ends up trailing the wrong hearse after being stopped by a red light. Convinced the burial party he discovers is an act, he accuses the mourners and the priest before realizing his mistake. Bough rescues him by pretending that English is an escaped asylum inmate.
The pair then uncovers the mastermind of the theft, French prison entrepreneur and descendant of William the Conqueror, Pascal Sauvage (John Malkovich). English reports his suspicions to the head of MI7, Pegasus (Tim Pigott-Smith), who dismisses his concerns as absurd. In the car park, one of Sauvage's henchmen attacks English and Bough, and escapes when English mistakenly attacks Bough. English and Bough infiltrate Sauvage's headquarters via parachute, but English lands on the wrong building, abseiling the identical London Hospital. He holds several staff and patients at gunpoint, before realizing his mistake.
English activates a DVD player, exposing Sauvage's plan to instate himself as King, using an impostor to impersonate the Archbishop of Canterbury(Oliver Ford Davies). After English accidentally injects himself with muscle relaxant, he and Bough are rescued from two of Sauvage's men by Lorna. She turns out to be an Interpol agent, also on Sauvage's tail (every major convict released from one of Sauvage's prisons in the last six months has been employed by one of his companies). Along with Bough, they gatecrash a party held by Sauvage. The muscle relaxant not yet worn off, English accidentally insults the Foreign Secretary (Jenny Galloway). One of the henchmen reports English to Sauvage, a friend of English's unwitting boss, who dismisses Bough and English. Sauvage decides that English has found out too much about his original plan, and sends his henchmen to force the Queen to sign a letter of abdication by putting a gun to her pet dog. The signature of abdication also nulls the Royal Family's and the line to the throne's right to the Crown; hereby, as planned, making Sauvage the automatic heir to be King. He acts surprised when informed by the Prime Minister that the position of monarch now belongs to him.
Lorna visits English at his flat, as his mission was reassigned to her, and persuades English to join her. They travel to France, infiltrate Sauvage's chateau, and overhear his proposal to turn the United Kingdom into a giant prison. However, English accidentally triggers a microphone, alerting Sauvage to their presence. In an attempt to steal an incriminating DVD, English accidentally drops it onto a tray full of identical discs, and takes what turns out later to be the wrong one. Taken hostage, the two agents are freed by Bough and return to England on the day of the coronation.
At Sauvage's coronation, English sneaks in disguised as the representative of the English bishops. He publicly accuses Sauvage of treason, and unaware that the fake Archbishop is no longer being used, English attempts to pull off the Archbishop's face, believing it to be a mask. Failing this, English pulls down the Archbishop's trousers to look for a tattoo, borne by the imposter, that says "Jesus is coming, look busy". English then radios to Bough to tell him to play the DVD they retrieved. Bough does so, resulting in three-quarters of the world's population watching English, in a shower cap and underpants, dancing and miming along to "Does Your Mother Know" by ABBA. English escapes, but comes back, swinging from a wire above Sauvage and the Archbishop, grabbing the crown before it touches Sauvage's head. Sauvage reveals his true intentions to London by pulling a gun and shooting at English, telling London that it will stand in line and do what he's told no matter what, including letting him turn the country into a prison. In the following struggle, English is inadvertently crowned instead. He places Sauvage under arrest, reveals the plot to the Queen and allows her to return to the throne, in return for a knighthood.
The film ends with English driving Lorna to the top of a mountain somewhere in the south of France where Johnny accidentally presses the eject button while about to kiss her, and Lorna shoots into the sky. There is also a short scene in the credits showing Lorna landing in a swimming pool where Bough is sitting and as the orange haired criminal described earlier by English lowers his newspaper.