At the 1972 Munich Olympics, the Palestinian terrorist group Black September kills eleven members of the Israeli Olympic team. Avner Kaufman, a Mossad agent of German-Jewish descent, is chosen to lead a mission to assassinate 11 Palestinians allegedly involved in the massacre. At the direction of his handler Ephraim, to give the Israeli government plausible deniability, Avner resigns from Mossad and operates with no official ties to Israel. His team includes four Jewish volunteers from around the world: South African driver Steve, Belgian toy-maker and explosives expert Robert, former Israeli soldier and “cleaner” Carl, and Danish document forger Hans. They are given information by a French informant, Louis.
In Rome, the team shoots and kills Wael Zwaiter, who is living as a poet. In Paris, they detonate a bomb in the home of Mahmoud Hamshari; in Cyprus, they bomb the hotel room of Hussein Abd Al Chir. With IDF commandos, they pursue three Palestinian militants—Muhammad Youssef al-Najjar, Kamal Adwan, and Kamal Nasser—to Beirut, penetrate the Palestinians’ guarded compound and kill all three.
Between hits, the assassins argue about the morality and logistics of their mission, expressing fear about their individual lack of experience, as well as ambivalence about accidentally killing innocent bystanders. Avner makes a brief visit to his wife, who has given birth to their first baby. In Athens, when they track down Zaiad Muchasi, the team finds out that Louis arranged for them to share a safe house with their rival PLO members and the Mossad agents escape trouble by pretending to be members of foreign militant groups like ETA, IRA, ANC, and the Red Army Faction. Avner has a heartfelt conversation with PLO member Ali over their homelands and who deserves to rule over the lands; Ali is later shot by Carl while the team escapes from the hit on Muchasi.
The squad moves to London to track down Ali Hassan Salameh, who orchestrated the Munich Massacre, but the assassination attempt is interrupted by several drunken Americans. It is implied that these are agents of the CIA, which, according to Louis, protects and funds Salameh in exchange for his promise not to attack US diplomats. Meanwhile, attempts are made on the assassins themselves. Carl is killed by an independent Dutch contract killer. In revenge, the team tracks her down and executes her at a houseboat in Hoorn, Netherlands. Hans is found stabbed to death on a park bench, and Robert is killed by an explosion in his workshop. Avner and Steve finally locate Salameh in Spain, but again their assassination attempt is thwarted, this time by Salameh’s armed guards. It is implied that Louis has sold information on the team to the PLO.
A disillusioned Avner flies to Israel, where he is unhappy to be hailed as a hero by two young soldiers and then to his new home in Brooklyn, where he suffers post-traumatic stress and paranoia. Concerns continue to grow when he speaks to Louis’s father by phone and it is revealed he knows his real name and promises no violence will come to him from his family. He is thrown out of the Israeli consulate after storming in to demand that Mossad leave his wife and child alone. Ephraim comes to ask Avner to return to Israel and Mossad, but Avner refuses. Avner then asks Ephraim to come to dinner with family, to break bread as an allegory to make peace, but Ephraim refuses, perhaps as a sign that neither side will reconcile.