Two separate bookies fall victim to unseen assassins, while a young man meets his end at the hands of a sniper. In a bus terminal, he encounters Goodkat (Bruce Willis), who recounts the tale of Max and the Kansas City Shuffle—a cautionary story from two decades prior. Max, portrayed by Scott Gibson, found himself in deep with the mob after betting on a rigged horse race. Unbeknownst to him, the mob controlled both sides of the gamble, causing Max to unwittingly bet against himself. With the race's outcome predetermined, and the news leaking about the rigging, the mob retaliated by eliminating Max, along with his wife and their young son, Henry. Goodkat introduces the concept of the "Kansas City Shuffle," a deceptive double bluff, and subsequently tricks and kills the young man, disposing of the body in a truck.
Meanwhile, in New York City, Slevin Kelevra (Josh Hartnett) is temporarily residing in his friend Nick Fisher's apartment. Under the impression that Nick was expected to meet him, Slevin finds himself perplexed by Nick's unexplained absence and the fact that the apartment door stands ajar. When Lindsey (Lucy Liu), Nick's neighbor, visits, she hints at Nick’s potential disappearance. Shortly after her departure, Slevin is seized by two henchmen, Elvis (Dorian Missick) and Sloe (Mykelti Williamson), who mistake him for Nick. They transport him to meet The Boss (Morgan Freeman), who has a vendetta against Nick for a gambling debt amounting to $96,000, which Nick owed after passing on his debt to The Boss's now deceased bookie.
The Boss commands Slevin—a case of mistaken identity—to either repay the debt or assassinate the son of his rival, The Rabbi (Ben Kingsley). The Boss believes that The Rabbi orchestrated the killing of his own son, the tensions between the two escalating. Upon returning to the apartment, Slevin is once again abducted, this time by The Rabbi's henchmen. Like The Boss, they incorrectly identify him as Nick and demand he settle another debt of $33,000.
Slevin declares to The Boss his intention to assassinate The Fairy, while the narrative reveals that Goodkat is intricately entwined in both rival factions, with ulterior motives to eliminate Slevin once The Fairy is dealt with. Lindsey, who works as a mortuary attendant, shares with Slevin about a bookie’s corpse recently admitted, theorizing that Nick might have been involved in those killings and has since gone into hiding, leaving Slevin in a precarious position.
During their dinner, Slevin arranges a rendezvous with The Fairy, and while in the midst of his plans, he is approached by Detective Brikowski (Stanley Tucci), who is deep into an investigation regarding both mob bosses and has noted the return of Goodkat after twenty years, which raises suspicions about their connections. As Slevin identifies himself more completely during the detective's questioning, his plot thickens.
At the scheduled date with The Fairy, Slevin takes action and fatally wounds him. Just then, Goodkat appears, seemingly ready to finish Slevin off but ultimately kills The Fairy instead, exposing their covert collaboration. They move swiftly, using Nick Fisher's corpse to fabricate Slevin's demise while detonating the apartment to cover their tracks. Capturing both The Boss and The Rabbi, they awaken binded in The Boss's luxurious penthouse. The Rabbi attempts to convince The Boss of their lack of involvement in the past murder but is ultimately exposed as a pawn in Goodkat’s greater scheme.
As the layers of duplicity are peeled back, Slevin reveals his true identity—he is Henry, the slain Max's son. The mobsters who executed Max are none other than The Boss and The Rabbi themselves. Goodkat, instead of killing Henry, opted to nurture him after a moral awakening when he was initially sent to finish the boy off.
Fast forward a score later, Slevin informs those left standing that he and Goodkat have eliminated the mob's bookies and pilfered their records to uncover Nick Fisher's ties to both sides, leading to their meticulous revenge scheme. With cunning strategy, Slevin has eliminated The Boss's son to instigate a fight between the two mob factions, eventually luring them both to their ultimate fates—murder at the hands of Slevin, who suffocates The Rabbi and The Boss in a similar fashion to how they dispatched his father.
Detective Brikowski, unaware of the connections running deep in his past, learns the origin of Slevin Kelevra—an allusion to Slevin's father's ill-fated bet. As Brikowski learns the truth of his past misdeeds, his fate intertwines with Slevin again, ending the cycle of vengeance and despair.
In an epilogue of sorts at the bus terminal, Slevin encounters Lindsey again, revealing a twist: Goodkat's intentions to keep her alive were complicated. They've orchestrated an elaborate deception. Goodkat uplifts Slevin's father's old watch to him before disappearing among the throng. The tale concludes at a reminiscent juncture, harking back to that fateful moment where Goodkat first chose to spare young Henry, as a song titled "Kansas City Shuffle" plays softly in the background.
