Harry (Sam Douglas), a British arms dealer, is seen in bed with a prostitute named Rena (Shivani Ghai). While toying with Harry's pistol, she unloads it but replaces the empty magazine. Harry's bodyguard Ewan (Sean Bean) is a British Secret Service Agent. Harry and Ewan travel to a bank, transporting a briefcase of Semtex. The men are followed by two terrorists, Ash (Abhin Galeya) and Ibrahim (Mens-Sana Tamakloe). Ibrahim approaches Harry and Ewan from the top of a staircase, shooting at them. After Ash shoots Ewan twice, Harry tries to shoot Ash, only to discover there are no bullets in his gun. Ash kills Harry and takes the briefcase of Semtex. However, Ewan manages to shoot Ash in the arm; but, before he can apprehend him, Ash returns fire and escapes with the briefcase.
Ash sews the stolen Semtex into a jacket along with a detonation device. He gives the jacket to Adel (Shane Zaza), who goes to a popular London restaurant and detonates the bomb. Being the only person who knows about the stolen explosives, Ewan is tasked by his two Secret Service superiors Charlotte (Charlotte Rampling) and Scott (James Fox) to find and eliminate the terrorists who created the bomb. His mission is off-the-books and unknown even within the Secret Service. He is given an assistant, rookie agent Mark (Tom Burke). Ewan finds Rena and beats her for any information she has about Harry. She tells Ewan and Mark that a man she frequented, Paul, paid her for information about Harry and to unload his gun. Ewan, Mark, and Rena go to Paul's house where Rena tries to aid Ewan and Mark in capturing Paul. However, Paul kills her and attempts to detonate a suicide jacket but is killed by Ewan.
At a cafè, Ash sees Kate (Tuppence Middleton), his former lover, and they exchange numbers. A series of flashbacks are shown from six years ago, where it is revealed that Ash and Kate were dating at university, where they both studied law. At the school, Nabil (Peter Polycarpou), a Muslim extremist, befriends Ash and asks him to join the pro-Muslim student group he heads. Ash and his friend Yussif (Chris Ryman) join the group and are exposed to Nabil's anti-Western teachings. Later that night, when Ash is at a bar, he sees Nick (Chris Geere) drinking and hitting on Kate. He argues with her but ultimately forgives her. Ash returns to the bar the following day and sees Nick, who insults him and says that he slept with Kate. Ash beats Nick up and goes to his apartment and breaks up with Kate. Nabil continues to brainwash Ash.
In the present, Ewan and Mark are sent to an abandoned building they are told is the home of a terrorist. Ewan confronts the man they find there (Jeetandra Lathigra) and interrogates him. The man begs for mercy, but Ewan sets him on fire and leaves him to burn to death. Searching the building, Ewan takes the man's jacket.
A series of flashbacks cut to three years earlier, where Nabil senses Ash's readiness to do more for the cause. Nabil tells Ash to participate in the punishment of Sgt. Glen Conlan (Glenn Wrage), an ex-soldier living alone on a farm, who he says killed and tortured Muslims throughout the Middle East. An experienced foreign operative named Amin (Silas Carson) is flown into the UK; Ash and his friend Yussif are instructed to act as his local guides and assistants. They travel to Conlan's farm. Yussif confronts Conlan in a barn but is stabbed in the face. Ash then chases Conlan and knocks him unconscious. Ash searches the house and finds a woman with a baby but does not tell Amin about them. Amin then searches the house again and kills the woman and her baby. Ash and Amin take Conlan to an abandoned building, where Ash films Amin beheading Conlan.
Ewan and Mark go to a housing estate, where they are noticed by Ash and another man wearing a bulky jacket. The unknown man takes off running, and Ash gets away on his motorcycle. Mark chases after the unknown man and shoots him dead. Mark and Ewan are told by Charlotte that the Secret Service has found out about their covert mission and is hunting them. Later, when Ewan is sleeping in a hotel, Mark breaks in and tries to kill him. After a fight, Ewan stabs Mark; but Mark refuses to tell Ewan who sent him. Ewan then kills Mark. Ewan realises he is now alone and must stop the terror cell before he is killed. Using Mark's earpiece, he discovers that whoever Mark was working for is facilitating the next bombing.
Ash and Kate get back together after six years of being apart. However, Ash sees his work with Nabil as more important and leaves Kate for a final suicide mission. Nabil tasks Ash with killing the head of a pro-Iraqi War think tank at his daughter's wedding in London. Ash makes a video explaining his reasons justifying his planned suicide attack. He travels to the wedding reception but is confronted by Ewan. Both are wounded in a fight, but Ash gets away. Disguising himself as a waiter, Ash makes his way to the reception's head table. Moments before Ash detonates his jacket bomb, he is shot by Ewan. After disabling the detonator, Ewan leaves the hotel. At the exit, Ewan notices men in suits delivering luggage on a trolley into the hotel lobby and then driving away from the hotel. Moments later, a bomb hidden in this luggage detonates in the hotel lobby, killing Nabil's targets.
In the epilogue, Ewan finds a safe deposit box key in the jacket of the man he killed earlier. He finds the box and its contents: a folder and video camera. He watches the tape, which shows footage of the man Ewan set on fire saying that he is an English citizen named Hussein Malik, who is an undercover Secret Service agent like Ewan. Ewan, distraught, goes back to the hotel room where he killed Mark and finds Charlotte's lighter in Mark's shirt. He realises that Charlotte hired Mark to kill him and framed Scott for being corrupt to cover any trace of her covert mission. Ewan confronts Charlotte at her countryside mansion and kills her, framing her death as a suicide.Sean Bean as Ewan
Abhin Galeya as Ash
Charlotte Rampling as Charlotte McQueen
Peter Polycarpou as Nabil
Tom Burke as Mark
Tuppence Middleton as Kate
Michelle Ryan as Emma
Sam Douglas as Harry
James Fox as Scott Catesby
Tariq Jordan as Paul
Shivani Ghai as Rena
Chris Ryman as Yussif
As of 3 February 2014, Cleanskin held a critical approval rating of 53% on Rotten Tomatoes.