The movie opens with the McManus brothers, two very religious and close Irish fraternal twins who work at a meat packing plant. Both are polyglots, able to speak Russian, Latin, Italian, French, Irish, German, English, and Spanish. The setting is a version of modern day Boston, which has been corrupted by gangland violence as a result of the presence of the Russian and Italian mobs.

On St. Patrick's Day, Connor and Murphy, in a pub, get into a fight with three Russian "soldiers", beating them up with the help of the other patrons. The morning after, two of the armed mobsters seek revenge on Connor and Murphy. Connor is handcuffed to the toilet while Murphy is taken outside the building for his execution. Connor escapes, drops the toilet on the hit man, and knocks the other hit man to the ground. Murphy then checks to see if Conner is okay, sees the mobster stir and then beats him to death with the toilet tank lid. Murphy then proceeds to pick both mobsters clean of their guns, jewelry, money and electronics.

Since the mob was involved in the incident, an FBI agent, Paul Smecker, is assigned to the case. Smecker surmises that the death of the two mobsters was not a professional hit, but probable self-defense. Connor and Murphy decide to clear their names and arrive at the police station. The police, as well as the local news, see Connor and Murphy as heroes. The police station is surrounded by reporters, so the brothers decide to spend the night in a holding cell in order to avoid the press. That night in the cell, they receive a vision from God telling them to hunt down wicked men so that the innocent will thrive.

The next morning, using the pager from the dead Russian mobster, Connor learns of a meeting of Russian syndicate bosses at a Boston hotel. Wearing masks and carrying a variety of weapons and tools, the two crawl through the ventilation ducts of the hotel and accidentally crash through the ceiling into the middle of the mob gathering. Entangled in the rope and hanging upside down, they quickly take out the nine bosses and underbosses, saving the leader (later called "Fat/Fag Man" by a detective) for last. They recite a short prayer and kill him with two gunshots to the back of the head. The brothers place coins on the dead men's eyes.



Rocco, in disguise as the hotel's room service deliveryman, then knocks on the door. He had been given a "big break" by Papa Joe Yakavetta, head of the Yakavetta crime family, and ordered to kill the top Russian mob leaders at the hotel. He had been told there would only be two Russians present, and was given a six-chamber revolver to kill 9 people. After much convincing on the part of the brothers and a run-in with two of his mob buddies at a local diner, he realizes that he was set up and convinces the brothers to let him join the team due to his connections and knowledge of the habits of his former employers.

Smecker is called in to investigate. Smecker pinpoints the cause as "bad television"; Connor and Murphy appear to have gotten many of their ideas from television. He announces coins were placed over the victims eyes because the ancient Greeks and Romans did this; they believed that the dead had to pay the boatman (Charon) to get across the river of the dead (Acheron or Styx).

After hunting down Vincenzo Lipazzi, underboss of the Yakavetta crime family, in a strip club, the three vigilantes then proceed to go on a series of increasingly violent missions, cleansing the city of the most vicious, merciless criminals. Papa Joe contracts Il Duce ("The Leader", in Italian, and original nickname of Benito Mussolini), the most feared killer-for-hire that has ever been used in the Yakavetta Family. In a gun battle, the three barely manage to survive, and Rocco's finger is shot off as they struggle to escape the scene.

Using Rocco's finger from the crime scene, Smecker discovers who the Boondock Saints are. By this time he has found he agrees with their vigilantism, but still feels bound by his duty as a law enforcer. He earns the brothers' trust and is contacted by them, agreeing to help them take down Papa Joe.

Throughout the film, the gradual discovery of the brothers' actions as Smecker investigates becomes sychronized with Smecker's real time. In the case of the Russian mafia peons, Smecker hears the story afterward when the twins confess the story. In the next case, Smecker is first shown theorizing, and then the scene cuts to a flashback of the brothers breaking through the air vent into the presidential suite of the Copley Plaza Hotel. During the live porn show scene, clips of the twins and Rocco shooting up the men in the booths are shown in tandem with Smecker investigating the scene. Later, when Rocco and the twins first encounter Il Duce, while Smecker investigates, the clips are superimposed over one another as if Smecker were there at the same time.



Later the McManus brothers, Rocco, and Smecker all infiltrate the Yakavetta headquarters to finish off the family. The brothers and Rocco are caught and bound in the basement, while Smecker, posing as a female prostitute, takes out several mobsters. Rocco is shot and killed by Papa Joe. The brothers escape from their chains but are too late to save Rocco. As they say their family prayer over his body, Il Duce arrives and sneaks up behind them. As he repeats the family prayer with them, it is revealed that Il Duce is actually the father of the brothers. He then joins them in their mission to kill all wrongdoers.

Papa Joe is sent to trial for his many crimes. Though there seems to be plentiful evidence of his crimes, the reporters on-scene anticipate his acquittal due to his "Gotti-esque" demeanor. The trial is forcibly interrupted when the two brothers and Il Duce, aided by Agent Smecker and three detectives, infiltrate and lock down the court room. After a speech stating that they intend to eradicate evil wherever they find it, they kill Papa Joe in the middle of the courtroom. As the spectators flee from the scene, the brothers and the Duke make their escape. The media dubs the three The Saints, and the movie ends with various people reflecting on the question "Are the Saints ultimately good, or evil?"