Agent 47 has left behind his life as an assassin and retreated to a church in Sicily to seek peace. He works as a gardener for Father Vittorio, his best friend and mentor. 47 attends a confession to admit his sins, but Vittorio understands and believes 47 is decent at heart. Father Vittorio is kidnapped and a ransom note is left for 47. 47 decides to go back to his old job as an assassin to track down Father
Vittorio. He contacts his agency, who thought he was dead, and makes a deal with his handler, Diana. He will work for them if the agency can help him locate Father Vittorio. They accept the deal.
Diana informs 47 that Father Vittorio was kidnapped by a Sicilian Mafia capo named Giuseppe Giuliano. The man is holding the priest in a cell under his mansion, dubbed Villa Borghese. 47 infiltrates and kills Giuliano, but fails to find his friend. He is later told that a satellite image shows Father Vittorio being taken away by 'Russian-looking types in uniform'.
47 works with the Agency to repay their attempt to find Vittorio. After both sides are satisfied the deal is fulfilled, 47 negotiates for a pay raise and continues to accept contracts. He travels to different countries, including Russia, Japan, Afghanistan, Malaysia and India, to carry out his missions, assassinating the assigned targets ranging from terrorists and criminal bosses to enemy agents and generals. Eventually 47 gives up his search for Vittorio, believing him to be dead.
47 eventually learns that Vittorio's kidnapping was a ploy orchestrated by Russian mafioso Sergei Zavorotko, the brother of one of the men 47 was cloned from, to lure 47 out of retirement. Zavorotko, who has ties to the Russian government and military, had recently purchased a nuclear warhead on the black market and needed to silence everyone involved in the deal; all of 47's targets were individuals involved in the transaction, and Zavorotko was responsible for hiring 47 on all of the jobs. 47 attempts to kill Zavorotko, but is ambushed by 17, one of the prototype clones made before 47. 47 kills 17 and pursues Zavorotko back to Sicily, where he is using Father Vittorio as a lure to draw 47 out into the open.
Infiltrating Vittorio's church, 47 discovers it being patrolled by several of Zavorotko's henchmen. 47 kills them all and eventually corners and kills Zavorotko as he holds Father Vittorio hostage in the church's confessional. Vittorio gives 47 his rosary and begs him to follow a good path. 47, having decided he is incapable of finding inner peace, leaves the rosary on the church door and resumes his life as a hitman.