Johnny English (Rowan Atkinson) has been training in Tibet following a botched mission in Mozambique when he is summoned by MI7. Under his new boss Pamela Thornton (Gillian Anderson), codename ‘Pegasus’, he is put on a mission to investigate a plot to assassinate the Chinese Premier during scheduled talks with the Prime Minister. He meets fellow agent and old acquaintance Simon Ambrose (Dominic West); MI7′s resident quartermaster, Patch Quartermain (Tim McInnerny); and junior agent Colin Tucker (Daniel Kaluuya), who will be English’s new assistant.
In Hong Kong, English finds ex CIA agent Titus Fisher (Richard Schiff), who reveals himself to be a member of Vortex, who were responsible for sabotaging English’s Mozambique operation. Vortex holds a secret weapon that requires three metal keys to unlock. But when he reveals his key, Fisher is killed by a grey haired woman (Pik-Sen Lim) disguised as an apartment cleaner, and another guy steals the key.
English chases the thief across Hong Kong, but loses him when the culprit leaps over a ventilator. However, recalling his Tibetan training, English simply slips into the gap between the ventilator and a wall. He continues the chase by means of easy solutions to hazardous routes the thief takes – for example, when the criminal slowly climbs down bamboo scaffolding, English simply takes an elevator. However, on his flight back to London, English is tricked by another Vortex operative disguised as a flight attendant, and is humiliated in a meeting with the Foreign Secretary and Pegasus when he attempts to present the key and the plans. He then mistakes Pegasus’s mother to be the cleaner assassin and attacks her at Pegasus’s daughter’s birthday party.
Kate Sumner (Rosamund Pike), MI7′s behavioral psychologist, uses hypnosis to help English recall his suppressed memory of the Mozambique incident, revealing another Vortex operative, Russian spy Artem Karlenko (Mark Ivanir), who is masquerading as millionaire Sergei Pudovkin. English and Tucker meet Karlenko at an exclusive golf course outside London. However, mid game, the cleaner assassin critically injures Karlenko. As English and Tucker fly by helicopter, the assassin shoots out the navigation system with a Gatling gun disguised as a golf bag. When asked by authorities about their location and altitude, they simply spot a street sign saying Runstock and say just that. They lower the chopper to less than a metre to easily identify altitude.
They simply follow a road at low altitude to the town of Dingham, where there is supposed to be a hospital. When Karlenko almost passes out, English and Tucker keep him awake with an awkward rendition of Don’t Give Up on Us. After landing on a moving ambulance, the three finally reach Dingham Hospital. Atop the ambulance, Karlenko reveals that the Vortex third key holder is a mole inside MI7, and then dies.
At MI7, English learns that talks between Britain and China will be conducted at a heavily guarded fortress called Le Bastion in the Swiss Alps, in order to gain assistance against the development of nuclear weapons in Southeast Asia. Over dinner, English confides with Ambrose about the mole, not knowing that Ambrose is the actual mole. Ambrose tricks English into thinking Quartermain is the traitor, and despite Tucker confronting Ambrose in the bathroom, English dismisses Tucker and lets Ambrose go free, giving him Karlenko’s key. At a church, English confronts Quartermain, but realises he has been framed as the traitor.
He escapes the MI7 operatives using Quartermain’s enhanced wheelchair, and hides at Sumner’s flat. After reviewing the footage of the Mozambique mission, Sumner realises the assassin behaved abnormally, and that Vortex has a drug called timoxeline barbebutenol that makes the person suggestible to mind control before killing them. Ambrose picks up Sumner to go to the fortress event, knowing that English had been hiding in the flat.
When English realizes Ambrose’s treachery is actually very real, he spots the cleaner vacuuming Sumner’s flat. When he hides behind a door, a chainsaw attached to the vacuum cleaner saws straight through the door. Luckily, English escapes the assassin via a garbage chute and makes for Tucker’s apartment. Not much later, Ambrose, accompanied with the other leader of Vortex, meets with Vortex’s current client and agrees for 500 million USD to be transferred to Ambrose’s bank account.
In Tucker’s flat, English persuades him to rejoin him to infiltrate Le Bastion. After getting in the gates, English accidentally activates a distress beacon that alerts the guards of the fortress to their presence. On English’s command, Tucker punches his superior several times and deliberately misses English with a gun, saying to the Swiss guards that he killed English. Having been taken to Le Bastion, English manages to get out of the bag that holds him. English warns Pegasus of the threat, but unknowingly imbibes the drink containing the drug. Ambrose tells English to subdue Pegasus, which he does with a punch to the face.
Assigning English to be the Prime Minister’s bodyguard inside the safe room, he orders him to kill the Chinese Premier using a pistol disguised as lipstick, which was hastily used despite it being intended for Thornton. However, English attempts to resist the drug. Tucker arrives and interrupts Ambrose’s communication feed with a radio channel playing the song ‘Word Up’, but Ambrose resets the communication, exposing himself to the Chinese Premier in the process. English resists again and shoots Ambrose, who dodges and escapes, but the chemical enters its lethal stage, and English falls to the floor. Sumner arrives and is able to revive English with a passionate kiss.
With Ambrose heading down the mountain, English pursues him by parachuting and then snowmobilling down a mountainside. The two spies fight in an aerial tram, but English prevails after recalling his training in Tibet where he was repeatedly kicked in the crotch, but falls off the lift. Ambrose shoots at English, but English mistakenly believes his spy umbrella is the D7 bulletproof shield.
Upon opening it, he accidentally triggers the umbrella, which is really the T2 rocket launcher, and destroys the lift, killing Ambrose. Later on, Vortex is shut down and English is to have his knighthood reinstated by the Queen. During the ceremony, the Queen is revealed to be the killer cleaner again, which leads English to attack the real Queen by accident, realising his mistake only when the killer cleaner is finally caught by the others.
