The film opens with a whimsical fantasy sequence featuring Johnny English, an incompetent British Intelligence agent, who imagines himself as "Agent One." In his daydream, he covertly infiltrates a building, distracts two guard dogs with toys, takes out two guards, and flirts with a woman who poses a threat. Just as he is about to kiss her, he is brought back to reality by the actual Agent One (Greg Wise), who is relying on English to prepare mission documents. After being assured that English has personally verified the submarine hatch codes, Agent One departs on a mission, a journey that ends tragically when he dies due to a malfunctioning hatch. In a twist of fate, a bomb eliminates all of Britain's remaining agents, who are attending Agent One's funeral, leaving only the hapless English behind, unnoticed as he escapes the scene in the hearse.
As the audience learns more, it becomes clear that before his demise, Agent One was onto a dangerous scheme involving the theft of the Crown Jewels. Seizing the opportunity to solve the case alongside his much more competent assistant, Angus Bough, English sets off on an investigation. During this time, he becomes infatuated with the enigmatic Lorna Campbell, whom he encounters during the unveiling of the restored Crown Jewels, where he is assigned as the security head.
A power outage ensues as chaos strikes. In an attempt to cover up his mistakes, English unexpectedly knocks out the chief of security and pretends to battle a criminal with vibrant orange hair, few teeth, distinct scars, and an eye patch. Despite their efforts, English and Bough find themselves outmatched as they chase the thieves but are hindered when English accidentally ejects his pistol’s magazine. When he mistakenly takes a funeral procession for a ruse, Bough saves him by pretending English is an escaped asylum inmate.
Their investigation leads them to discover the brains behind the Crown Jewels heist, the Pascal Sauvage, a French prison mogul and a descendant of William the Conqueror. When English informs MI7's head, Pegasus (Tim Pigott-Smith), about his suspicions, he is met with skepticism. In a tense showdown in a parking lot, he and Bough are ambushed by Sauvage's henchman, Klaus Vendetta, who escapes when English mistakenly attacks his own partner.
While trying to infiltrate Sauvage's base, English lands on the wrong building, inadvertently taking hostages before discovering his blunder. However, he manages to activate a DVD player that reveals Sauvage's plot to ascend to the throne by employing an impostor Archbishop of Canterbury (Oliver Ford Davies). After some comical mishaps, English realizes that Lorna is actually an Interpol agent, hot on Julien's trail due to the suspicious employment of released convicts from Sauvage's prisons.
Together with Bough, they crash a lavish party hosted by Sauvage. Unfortunately, still under the influence of a muscle relaxant, English mistakenly insults a government official. After being dismissed, Sauvage learns that English knows too much and plans to turn the Queen into a puppet monarch, forcing her to abdicate her throne.
In an unexpected turn, Lorna visits English at his apartment after receiving his mission. They team up and venture to France to infiltrate Sauvage's estate, where they overhear him plotting to convert the UK into a massive prison. Once again, English's antics lead to their capture, but they are saved by Bough, returning just in time for the coronation.
During the coronation event, English sneaks in disguised as a bishop, confronting Sauvage with accusations of treason. In the chaos, he mistakenly believes that the fake Archbishop is merely a mask, leading to ridiculous outcomes. He instructs Bough to play the incriminating DVD he retrieved, inadvertently broadcasting his own embarrassing dance to the world.
With a daring move, English swings in to secure the crown before it can touch Sauvage's head. Faced with the impending threat of Sauvage's reign, English engages in a struggle that ends with him claiming the crown and arresting Sauvage, ultimately allowing the Queen to reclaim her throne in exchange for a promised knighthood.
The film culminates with a charming moment where English drives Lorna to the summit of a mountain, only to accidentally hit the eject button in a comical mishap while attempting to kiss her. As the movie rolls on, a cheeky scene during the credits shows Lorna landing in a swimming pool next to Bough, with the orange-haired criminal from earlier casually reading his newspaper.
