The film opens with mass in a Boston Catholic church. Twin brothers Conner MacManus (Sean Patrick Flanery) and Murphy MacManus (Norman Reedus) pray while a sermon is read. As the priest begins his homily, the brothers approach the altar. They depart as the priest reminds the congregation that they should fear not just evil but also the "indifference of good men". The brothers conclude that the priest finally understands, with Conner saying, "I do believe the Monsignor's finally got the point." Murphy replies, "Aye".
Conner and Murphy work at a local meatpacking plant. While celebrating St. Patrick's Day in a neighborhood bar, three Russian "soldiers", led by Ivan Checkov (Scott Griffith), enter and order everyone to leave. In the ensuing bar brawl, Conner, Murphy, and the patrons humiliate the mobsters, who the next day ambush the brothers in their home. Murphy is dragged into a nearby alley to be executed, but Conner escapes to the roof and drops down with a toilet off the roof and onto the mobsters, killing them and rescuing Murphy.
The Russian mob's involvement summons flamboyantly gay FBI agent Paul Smecker (Willem Dafoe) to the murder case, and he surmises that the mobsters' death was not a professional hit but self-defense. As the police begin a manhunt for the killers, Conner and Murphy arrive at the police station to clear their names. During the initial interrogation, the brothers impress Smecker with their multilingualism (including Gaelic, Russian, French, Spanish, Italian, and German) while explaining the bar fight and subsequent self-defense the next morning. Smecker believes their story and allows them to stay overnight in a holding cell to evade the press. That night, Conner and Murphy receive a vision from God telling them to destroy all that is evil so that which is good may flourish.
The brothers resolve to rid Boston of "evil men" with the help of their friend and former mob package boy David "The Funnyman" Della Rocco (David Della Rocco). The brothers trade in the weapons and valuables stolen from the mobsters' bodies for their own, and use Conner's knowledge of Russian to locate a meeting between Russian syndicate bosses at a local hotel. Crashing into the room through an overhead air duct, the brothers draw their guns and fire, killing the 8 underbosses. Forcing the leader, Yuri "Fat Man" Petrova (Victor Pedtrchenko), who was the brothers' main target, to his knees, the brothers recite a short prayer.
Then they execute him, placing pennies over his eye sockets, in which both of his eyes were shot out. While the brothers are preparing to leave the hotel, they are surprised to find Rocco dressed as a bellboy knocking at the door with a tray of food. They pull him into the room, concealing their identity with masks, and threaten to execute him. Rocco, who is begging for mercy, says he was sent as backup by Italian mob boss Papa Joe Yakavetta (Carlo Rota). Eventually they reveal their identity to Rocco, who becomes appalled at seeing the dead Russian bodies in the room. Once again, Agent Smecker is brought to the front of the murder case. Smecker's theory is that the executions were the result of the feud between the Russian and Italian mobs.
The next day, the brothers try to convince Rocco that he was sold out by Papa Joe, because he was sent to the hotel with a six-shooter despite the fact there were 9 mobsters in the hotel room. Rocco soon realizes this after killing two of Yakavetta's men at a deli later on, who hint to Rocco that he really was sold out. In retaliation, Rocco and the brothers hunt down and kill Vincenzo Lipazzi (Ron Jeremy), underboss of the Yakavetta crime family at a local strip club. Also killed at the Strip Club are two street criminals with no connection to organized crime (thus disproving Smecker's mob war theory). The three vigilantes proceed on a series of increasingly violent missions, cleansing the city of criminals and others who have eluded justice. Papa Joe, believing that the mob killings are an act of revenge from Rocco, contracts the infamous contract killer Il Duce (Billy Connolly), to deal with the package boy.
As Smecker and his team investigate the scene of the killing of Lipazzi, Smecker is informed of the shooting that took place earlier in the day at the deli. However he is unable to connect this incident to the one at the strip club because at first one of Smecker's men said the shootings were not related, but Smecker realizes that different weapons were used at the deli. Rocco used a six-shooter at the deli, while he and the brothers later on used silenced pistols at the strip club. Smecker reveals that the shootings were related due to the fact that there were no witnesses at either scene, though at the strip club there was a stripper who went unconscious before Lipazzi was murdered. Angering Smecker, he leaves the deli and he warns that there will soon be related shootings carried out by the three vigilantes.
Rocco insist that he and the brothers murder a hitman that Rocco had briefly worked with. According to Rocco, the man was responsible for murdering an entire family and had burned their remains in a dumpster. They head to the hitman's house and murder all of his men. After a hand-to-hand fight, Rocco beats the hitman to death with a cue ball. As they leave the hitman's house through the front door, the trio is ambushed by Il Duce, and in a shootout the trio chase Il Duce away. Rocco's finger is shot off and each of the brothers receive serious gunshot wounds which they cauterize with a hot iron. Hours later at the crime scene, Smecker discovers the finger and takes it to conduct his own investigation. Discovering that it belongs to Rocco, whom he previously met, Smecker begins to unravel the mystery surrounding the various murders.
His sympathy for the brothers conflicting with his professional desire to bring them to justice, Smecker, who is homosexual, goes to a gay bar, gets drunk, and seeks advice from a nearby Catholic church. Bemoaning the futility of the courts that fail to punish evil men and his uncertainty with the MacManus brothers' actions in a confessional, Smecker is oblivious to the fact that Rocco, who has tracked Smecker to the church, is forcefully directing the priest's responses to preserve the Boondock Saints' identities. Conner sees Rocco follow the priest into the confessional and, disgusted with the blasphemy, pulls Rocco's head through the other confessional at gun point. In whispered tones, Rocco tries to explain to Conner the circumstance while still holding his gun to the priest's head. Smecker is advised, reluctantly by the priest, that the Saints are acting as messengers from God and that "the laws of God are greater than the laws of man." Inspired by the advice, Smecker decides to help the brothers.
Then the brothers contact Smecker on the phone and inform him that they, along with Rocco, would finish off Papa Joe Yakavetta that night. Things at first go to plan that night as the brothers and Rocco infiltrate the Yakavetta headquarters to finish off the family, but are captured by Papa Joe and his henchmen who recently arrived to protect Papa Joe. When Papa Joe comes down to the basement, Rocco curses him. Papa Joe decides to execute Rocco to intimidate the brothers, who free themselves and tend to Rocco while Smecker, disguised as a female prostitute, distracts the other mobsters. Smecker kills the remaining mobsters only to be knocked unconscious by Il Duce who mistakes Smecker for a woman. As the brothers say their family prayer over Rocco, Il Duce arrives and sneaks up behind them.
As he hears them recite the family prayer and sees that the man he was hired to kill (Rocco) is dead, he lowers his weapons and joins them. It becomes apparent that Il Duce is their long-lost father, as the brothers had previously refused to teach Rocco the prayer because it is only passed down in their family. He then joins them in their mission to rid the city of evildoers.
Three months later Papa Joe is sent to trial, and though there seems to be enough evidence to convict him, the reporters on scene anticipate his acquittal due to his charisma. The trial is forcibly interrupted when the two brothers and Il Duce, aided by Smecker and several police officers, infiltrate and lock down the courtroom. The three then publicly declare their mission to destroy evil and recite their prayer one last time, killing Papa Joe with several bullets. The media dubs the three "Saints", and the movie ends with various "man-on-the-street" interviews in which various Boston citizens reflect on the question "Are the Saints ultimately good or evil?"
"The Boondock Saints" is very watchable and keeps the viewer interested throughout with a strong story, frequent black humour and interesting visuals. Willem Dafoe steals the show and David Della Rocco is also very good. It's funny, touching, and even moving occasionally, not very politically correct, the acting is competent, with a clever balance of humor and tension, with phoney Irish accents. This gangster film may carry a message about self-help justice with elements of comedy, tragedy and morality. The "f" word is used almost 250 times, and the movie has received poor reviews from critics who bitch about poor acting, a sketchy plot, and too much violence. Jeff Danna composed the music, and Troy Duffy wrote the screenplay and directed.
