Psychopathic Villanelle—a young and prolific assassin—leaves a trail of high-profile murders across several countries. MI5 officer Eve Polastri connects a new assassination in Vienna to a series of such killings which she has been researching on her own time. Her theory that the assassin is a woman is dismissed by her superiors, but her unauthorised interview with the only witness confirms it. The witness is murdered while in a London hospital, along with a nurse and two guards, causing MI5 to fire Eve and her associate Bill. Impressed by Eve, Carolyn Martens, head of the Russia Section of MI6, recruits her for an off-the-books assignment to track the killer.

Following her assignment in Bulgaria, Villanelle's handler Konstantin is concerned about her increasing recklessness. He informs her that a covert MI6 task force, led by Eve, is investigating her string of assassinations. Eve realises that a nurse she saw at the hospital before the murders may be the killer. Carolyn introduces Eve to Kenny (Carolyn's son) who has been gathering evidence on the assassinations, and allows Eve furthermore to recruit Elena and Bill as her assistants. Villanelle forms a relationship with her neighbour Sebastien and carries out another murder, of a successful parfumier, at a dinner party in Paris.

Villanelle lures Eve to Berlin by using Eve's name while committing another murder, and trails Eve as she investigates it. Bill spots Villanelle and follows her to a nightclub. Before Eve can get to him, Villanelle stabs Bill repeatedly, killing him.

Konstantin punishes Villanelle for her recent unpredictable behaviour by making her work with two other operatives: Nadia and Diego. The three are to assassinate Frank Haleton, Eve's former MI5 boss, whom Eve has discovered is a mole. Eve and Elena rush to Frank's rescue, while Villanelle manipulates Nadia into killing Diego, then runs over Nadia with Diego's car.

Eve and Carolyn get Frank to a safe house, and he tells them that he is being paid by a shadow organisation "the Twelve" that uses Villanelle for purposeful destabilisation. There are hints that Elena and Kenny may have a romantic relationship. Villanelle breaks into Eve's home to talk to her and takes her phone, which Villanelle uses to track down Frank at the safe house and kill him. Konstantin tells Villanelle that Nadia is alive and has to be killed before she can be questioned.

Eve and Carolyn track down Nadia to a Moscow prison, and are allowed to speak to her due to Carolyn's camaraderie with two Russian Intelligence officers, one of whom is Konstantin. Eve and Carolyn offer Nadia a deal, but before she can accept, she is killed by Villanelle, whom Konstantin had transferred to the prison for that purpose.

Eve investigates Anna, Villanelle's former teacher, with whom she had a deep relationship before Villanelle killed her husband. Villanelle is broken out from prison, meets her new handler and is given her next target: Konstantin. Villanelle breaks into Konstantin's home but he escapes. Eve discovers that Carolyn secretly met Villanelle at the prison earlier that day, before she escaped.

Konstantin goes to Carolyn and Eve for help, fearing for his and his daughter's lives. Villanelle goes to Anna for her passport and money. Eve had taken the passport and left her a note. Villanelle gets angry, but Anna kills herself before Villanelle can. Villanelle calls Eve to come to a cafe and bring her passport and Konstantin. Eve complies and a fight starts in the cafe, during which Villanelle shoots Konstantin and escapes. Carolyn fires Eve from MI6, but Eve independently tracks down Villanelle to her Paris apartment. The pair confess their obsession with each other. Eve stabs Villanelle and Villanelle flees.

Continuing directly from the end of the first series, Eve searches for the wounded Villanelle. Without finding her, Eve is called back to London to investigate a murder case believed to have been ordered by the Twelve. Villanelle has a rough time as she makes her way from a Paris hospital to London.

Eve meets her new team and deduces that the murderer is not Villanelle, but a new assassin for the Twelve whom she nicknames "the Ghost". Villanelle is close to London, and tricks a man, Julian, into taking her home and helping her heal, but he tries to trap her at his house. After a few days she escapes, killing him and meets her new handler, Raymond.

Villanelle is ordered by Raymond to perform a clean assassination like the Ghost. She kills her target in a lift and delivers lipstick to Eve with the name "Love in an Elevator" to ensure that Eve knows who performed the assassination. Eve is struggling with balancing her job and her strained relationship with Niko.

The Ghost's body count is much larger than expected and appears to be based around Aaron Peel. Villanelle tries to get Eve's attention with an assassination in Amsterdam based on The Corpses of the De Witt Brothers, but is angered when Eve does not show up to investigate.

In a desperate attempt to get closer to Villanelle, Eve puts out a hit on herself, hiring Villanelle to do the job. Instead, Eve and Carolyn hire Villanelle to work with MI6. The Ghost is coerced by Villanelle into giving up information about who ordered the murder contract. Villanelle meets Niko and tells him about her and Eve in Paris.

Niko confronts Eve about what really happened in Paris. With new information about Aaron Peel, Villanelle goes undercover as a New Yorker named Billie to befriend Aaron's sister, Amber but there is conflict between Villanelle and Aaron.

Aaron apologises to Villanelle and invites her to go to Rome. Villanelle interrogates Niko whilst Eve visits the psychologist. In Rome, Villanelle discovers Aaron's plans but Eve becomes jealous of their relationship.

Villanelle discovers Aaron's dark secret and says the 'safe word'. Eve dresses as a cleaner to save Villanelle but she saves Eve instead. Raymond attacks Villanelle but she is saved by Eve, who kills Raymond. Villanelle and Eve escape to Hadrian's Villa (Teatro Marittimo, Tivoli, Lazio) and have an argument there. Villanelle reveals that she wanted Eve to kill Raymond to see how it feels to kill. Eve rejects Villanelle's plan for them to run away together and walks away. Villanelle shoots Eve and leaves.

Six months after the events in Rome, Villanelle has settled down in Spain and is about to be married when former assassin Dasha appears. Dasha trained Villanelle and now asks her to return to working for the Twelve. Villanelle asks to be promoted to the role of "Keeper" in return, which would make her more powerful than both Dasha and Konstantin. To prove her loyalty, she is tasked with killing a local political agitator in Barcelona. At MI6 Paul has been appointed to 'oversee' Carolyn's Desk. Meanwhile, Eve survives the shooting, but has left MI6 and now works at a Korean restaurant in New Malden. Kenny has also quit MI6 and now works as a journalist independently investigating the Twelve. Eve agrees to meet him for after-work drinks, but finds his office deserted. She discovers his dead body outside, having apparently been thrown from the roof by an unknown assailant.

Eve gets drunk at Kenny's funeral after learning his death was declared a suicide. She tries to access his phone, but is blocked by the password. Kenny's boss Jamie offers to unlock it in exchange for her co-operation in investigating Kenny's death. Carolyn approaches Eve separately, frustrated that she cannot investigate Kenny's death after being put on bereavement leave. She believes that Villanelle is active again. Eve hesitates, but ends up agreeing to help Carolyn. The two are unaware that Konstantin is eavesdropping on them. Meanwhile, Villanelle is assigned to mentor Felix, a promising young assassin. They infiltrate a children's birthday party to kill their target, but Felix diverges from the plan and Villanelle kills him. She returns home to find Konstantin waiting for her, and he informs her that Eve is alive.

Eve finds that Kenny had been looking into financial records and that a bank account in Geneva, used by the Chinese diplomat Villanelle killed in season 1, has suddenly become active again. Carolyn engineers a meeting with Henrik, a Swiss banker and her former flame, to find out who manages the account. The trail leads to Charles Kruger, a former Russian agent who disappeared at the end of the Cold War. Eve suspects that he is the Twelve's accountant. Villanelle tracks her down on a bus and the two briefly fight; Villanelle gains the upper hand, but Eve surprises her by kissing her before headbutting her. Eve realises that Villanelle might be in London to kill Carolyn. She tries to warn Carolyn as she visits Kruger, but she is too late. Disguised as a police officer, Villanelle kills Kruger. Eve returns to her apartment to find a stuffed toy reciting a recorded message from Villanelle.

Eve finds a connection between a murder committed by Villanelle and another death in 1974, and is disturbed by the delivery of a birthday cake sent by Villanelle. Konstantin tracks down Kruger's widow and convinces her to send him a file that Kruger had set aside as an insurance policy. He travels to Barcelona and gives Villanelle information on her family, promising her more if she kills Kruger's widow. Meanwhile, Niko leaves England for Poland to manage his PTSD. Eve repeatedly tries to get in contact with him, but receives no response. Dasha is approached by an agent of the Twelve who orders her to make sure Villanelle remains focused. She follows Niko to Poland and steals his phone, using it to lure Eve to his farmhouse. Dasha stabs Niko in front of Eve, but remains hidden from view. She leaves a message to make Eve think Villanelle is responsible as Villanelle arrives at her hometown in Russia.

Villanelle's return to her family home in Russia is met with surprise and suspicion from her extended family. She bonds with her reclusive brother Pyotr and her Elton John-obsessed half-brother Bor'ka, and reunites with her mother Tatiana. She settles into family life and for a time enjoys herself. Things come to a head when the family visit the local Harvest Festival; Bor'ka enters a cooking competition, but does not win. He confides in Villanelle that Tatiana shamed him for embarrassing her afterwards. Villanelle confronts Tatiana over her abandoning Villanelle at an orphanage as a child. Tatiana demands she leave before claiming that Villanelle's father, whom she adored, was in fact afraid of her. Heartbroken, Villanelle kills Tatiana before blowing up the house, sparing only Bor'ka and Pyotr. Villanelle leaves money for Bor'ka to buy tickets to an Elton John show and escapes aboard a train, where she starts crying and dancing in her seat to the music on her headphones.

Villanelle is promoted to Keeper by Hélène, an agent of the Twelve, and ordered to kill a Romanian politician. Disappointed and frustrated that the work is no different, she approaches Konstantin and asks to join his plan to run away. Konstantin is reluctant because his daughter Irina hates her. Villanelle and Irina bond over their shared dislike of their mothers. Paul assigns Konstantin to investigate Kruger's wife's death and tells him that the person who arrange the hit is the one they have been looking for. Carolyn continues her investigation into Kenny's death and is shocked to learn that Kenny believed Konstantin was his father. Meanwhile, Niko survives his attack but rejects Eve. Eve deduces that Villanelle did not attack Niko. She visits Dasha in Barcelona, who taunts her; Eve is unfazed and tells her that she knows she attacked Niko. Dasha returns to her apartment and finds an injured Villanelle. Villanelle admits that she wants to escape the life of a killer for hire. Konstantin prepares to flee with Irina but is horrified when she runs over her stepfather with a car.

Villanelle meets with Hélène over her commitment to the job. Villanelle asks for another assignment instead. She and Dasha travel to Aberdeen to kill an American businessman at a golf resort. After luring the American into the woods, Villanelle hits Dasha over the head with a golf club and leaves her for dead. Eve tracks Villanelle's credit card to Aberdeen and finds Dasha semi-conscious in the woods. Dasha admits to stabbing Niko and Eve is tempted to kill her by standing on her chest. Carolyn's aide, Mo, discovers something connecting Paul to the Twelve but he is killed by Rhian, an assassin for the Twelve. Meanwhile, Konstantin is frustrated by his inability to get Irina released from prison. He returns to England and is called by Villanelle to pick her up after she attacks Dasha. As they prepare to board a train, he begins having a heart attack. Villanelle promises to return for Konstantin, but abandons him instead, and he is found by Eve. As Villanelle's train leaves, she looks out the window to see Eve on the platform. She calls Eve. Konstantin wakes up in a hospital and finds Dasha in the bed next to him.

Villanelle approaches Carolyn and offers to become an informant for MI6; Carolyn rejects her when she cannot provide any information. Villanelle then asks Eve to retrieve a package Konstantin had hidden to aid his escape. Their meeting is interrupted by Rhian, who summons Villanelle to meet Hélène. Villanelle kills Rhian. Konstantin checks himself out of hospital and argues with Dasha over their handling of Villanelle. The stress causes Dasha to die of a heart attack. Konstantin reaches Eve when Paul calls him and demands to see him. They arrive at Paul's house to find Carolyn holding him at gunpoint and Villanelle joins them. Having seen a video of Kenny and Konstantin on the day Kenny died, Carolyn demands an explanation from Konstantin. He claims he tried to recruit Kenny into the Twelve to save him, but Kenny got scared and fell to his death. Carolyn eventually spares him and kills Paul. She concludes that she will never be able to stop the Twelve. Eve and Villanelle leave together. They make a pact to walk away and never see each other again, but the two stop walking and look back at each other.

An unspecified amount of time after the end of the third series, Villanelle has turned to religion in an effort to redeem herself and is living in a church in England with vicar Phil and his daughter May. Eve, still going after the Twelve and now working in private security, tracks down Konstantin, who is now mayor of a Russian town, and obtains a lead on Hélène. Carolyn, having been demoted after killing Paul, also continues to hunt down the Twelve and finds out someone has been killing its members. Frustrated with her lack of official powers, she enlists the help of Eve and later defects to Russia in search of more information. Villanelle invites Eve to her baptism, but she does not attend. Villanelle makes a surprise visit to Eve, but Eve does not acknowledge her efforts to change. Frustrated, Villanelle returns to the church and attempts to kill May by drowning her in the baptismal font but manages to stop herself. Later that night, Villanelle has a vision of Jesus in the form of herself in drag.

Guided by her vision of Jesus, Villanelle joins Phil, May and their congregation on a camping trip. Villanelle appears to make amends with May after the attempted drowning, and May confides in Villanelle that her father Phil is responsible for her mother's death by crashing their car while driving drunk. Villanelle reveals this to the rest of the congregation in an attempt to hold Phil accountable, but she is met with rejection. She later overhears Phil and May talking about her negatively, lashes out and kills them. She then leaves the campsite, abandoning her vision of Jesus. Meanwhile, Eve tracks Hélène to an apartment in Paris. She is aided by her colleague Yusuf, with whom she also has a casual sexual relationship. They travel to Paris, where Eve confronts Hélène in her apartment. Hélène reveals to Eve that she is responsible for the murders of the members of the Twelve that Carolyn uncovered. She is doing this to find the leader of the Twelve. Eve and Hélène agree to help each other.

Villanelle returns to London and breaks into Eve's hotel room. Eve, having returned from Paris, finds her there and rejects her calls for help, but allows her to stay in the room. Eve leaves to track down Hélène's car to a parking garage where she runs into a disgruntled ex-girlfriend of Hélène. Eve invites her for drinks in an attempt to obtain information on Hélène's target and learns she was married in Cuba to a presumably German man named Lars, before her relationship with Hélène. Eve believes Lars could be Hélène's target. Hélène meets with Pam, an assassin-in-training who expresses a wish to start working to escape her abusive family. After hesitation, Hélène agrees and assigns Konstantin as her handler. Using Eve's tablet, Villanelle arranges a meeting with Eve's psychiatrist friend Martin and holds him hostage at his home, forcing him to give her therapy. Martin tells her that her psychopathic tendencies were learned, and can possibly be unlearned. Eve returns to her hotel room and finds out Villanelle went after Martin. She meets Villanelle at Martin's home, shortly followed by armed police requested by Eve, who arrest and imprison Villanelle.

Villanelle is released from prison with the help of Hélène, who tells her that it is impossible to leave the Twelve and gives her a new assignment in Cuba. In Havana, Cuba, Villanelle kidnaps Carolyn, who has traveled there to interrogate Rustem, a member of the Twelve who survived an assassination attempt ordered by Hélène. She assaults Carolyn but spares her life after Carolyn reveals to Villanelle that she has known her since she was a child in the orphanage. Carolyn encourages Villanelle to interrogate and torture Rustem, who gives up the name of a restaurant before being killed by Villanelle. Carolyn runs into Lars at the restaurant, who is surprised to see Carolyn and flees. She tells Villanelle that she was in a relationship with Lars and that he is likely headed for Berlin. Meanwhile, Eve meets Hélène who confirms that Lars is in fact her target, and challenges Eve to find him before she does. While following up on a lead in Paris, she is contacted by Hélène who invites Eve to her apartment and taunts her with the news that Villanelle is out of prison. In response, Eve kisses Hélène and leaves the apartment.

In 1979, Carolyn and Konstantin attend an anarchist meeting in Berlin, led by Lars. When Lars is gathering ideas for names for their group, Carolyn suggests they name themselves after the number of founding members—twelve. Carolyn and Konstantin flirt, and eventually spend the night together. She later discovers that her father, a British spy, has committed suicide after being blackmailed. After learning that Konstantin is Russian, she confronts him at a lake. Konstantin says he is a KGB spy and responsible for blackmailing her father. Lars finds the two arguing and a fight ensues during which he falls into the lake and disappears, presumed dead.

In the present day, Villanelle murders the abusive husband of her Cuban hostess, then leaves Cuba to meet Konstantin in Margate in an attempt to locate Hélène. Eve acquires an old Super 8 film of Lars and his British girlfriend. Viewing the recording, she recognizes a young Carolyn. Eve abducts Hélène's daughter Chloe from Paris as a response to Hélène bailing Villanelle out of prison. Hélène retaliates by driving Eve out to Margate, where Eve is forced to watch Villanelle being struck by an arrow and falling unconscious. Eve runs to Villanelle and cradles her.

Villanelle's injuries are treated by Eve, Konstantin and Pam. Gunn, a Twelve assassin from Scotland who was also trained by Konstantin, might be behind the attack. An unsuspecting Villanelle later meets Gunn, who slips her a note stating that she was ordered to kill Villanelle by Hélène but chose to spare her, and that Hélène is in a hotel in Berlin. Eve travels to Berlin after being told by Villanelle that Carolyn and Lars are there, but only finds Hélène and follows her to her hotel room. Villanelle, who was already hiding in that room, kills Hélène in front of Eve. Still upset with Eve for having her arrested, Villanelle abandons Eve. She leaves for Scotland to meet Gunn after being given her location by Konstantin. Eve tracks down Carolyn and confronts her outside Lars' cabin near Berlin. Carolyn says that she is not part of the Twelve and that she is only there to get information out of Lars. To Carolyn's disappointment, Eve enters the cabin and kills Lars. Carolyn searches Lars' body to find a notebook. Villanelle arrives at the remote Scottish island where Gunn lives. She meets Gunn and asks if she can stay with her.

Villanelle wakes up on Gunn's island and accompanies Gunn on a hunting trip. The two exchange stories and kiss. Gunn immediately becomes attached to Villanelle, but Villanelle rejects Gunn upon learning that she is still loyal to the Twelve, and attempts to leave the island. Gunn responds by chasing Villanelle with a machete. Meanwhile, Eve is invited to karaoke by Yusuf, where she experiences flashbacks of her former husband and MI5 colleagues. Yusuf permanently leaves Eve after she tells him she cannot move on from her past. Eve visits Martin for guidance, who advises her to connect with the people who truly understand her. Eve receives a cryptic message on Hélène's phone and visits Konstantin, who tells her it is an announcement for a Twelve meeting. He advises her to bring Villanelle along with her and gives her the location of Gunn's island. Pam visits Konstantin after Eve leaves, and kills Konstantin on Hélène's final orders. A dying Konstantin reveals Hélène's death to Pam and asks her to deliver a letter and love declaration to Carolyn. Eve travels to Gunn's island and is ambushed by Gunn while Villanelle, who has hidden in the bushes, watches from nearby.

Eve blinds Gunn during their struggle, and she and Villanelle escape the island. They spend a loving day and night together travelling through the Scottish countryside to reach the Twelve meeting in London, after Eve convinces Villanelle to help her. Meanwhile, Pam delivers Konstantin's letter to Carolyn. Pam is offered a job by Carolyn, but she refuses and walks away. Carolyn, having followed clues in Lars' notebook, arrives at the Twelve's proposed meeting place shortly followed by Eve and Villanelle. Hélène's phone receives a message indicating that the meeting place has changed to a boat on the River Thames where a wedding is also taking place. At night, Eve and Villanelle board the boat, where Villanelle slaughters the present Twelve members while Eve distracts the wedding guests. Right afterwards Villanelle is shot by an unseen sniper. Villanelle saves Eve by shielding her and taking the shot as the two jump in the Thames, where Villanelle sinks into the depths with Eve unable to reach her. Carolyn, watching from a distance, acknowledges the assassination on a walkie-talkie. Eve resurfaces in the middle of the river and screams in anguish.