In 1980s Boston, Irish Mob boss Frank Costello takes a young Colin Sullivan under his wing, grooming him for the future. Years pass, and Sullivan infiltrates the Massachusetts State Police (MSP) as a mole for Costello. Meanwhile, Billy Costigan, another recruit at the police academy, is chosen by Captain Queenan and Sergeant Dignam to go undercover and embed himself within Costello’s criminal empire.
To solidify his cover, Costigan serves a stint in prison and commits various crimes, catching Costello’s attention. Sullivan, now a rising star in the MSP’s Special Investigation Unit (SIU), starts a relationship with police psychiatrist Madolyn Madden. On the other hand, Costigan’s efforts earn him a spot in Costello’s crew. Over time, Costigan’s role in Costello’s organization deepens, taking a toll on his mental health. Despite his growing instability, Queenan and Dignam urge him to continue the mission. During his court-mandated therapy sessions, Costigan grows closer to Madden.
Both the MSP and Costello suspect they have moles in their ranks. Costello assigns his men, including Costigan, to unearth the mole, while the MSP tasks Sullivan with the same mission. As the investigation heats up, Costigan uncovers a shocking truth: Costello is secretly an FBI informant. He shares this information with Queenan while also beginning an affair with Madden.
One evening, Costigan tails Costello to an adult theater, witnessing him pass an envelope to Sullivan, containing details about his crew. Costigan fails to identify Sullivan but realizes the mole’s proximity. Sullivan, sensing someone is tailing him, mistakenly kills an innocent man and escapes. With Costello’s paranoia escalating, Costigan fears his cover is about to be blown and contacts Queenan, requesting to end the operation. Sullivan, however, manipulates the situation, having Queenan followed while tipping off Costello’s gang.
Costello’s men intercept the meeting between Costigan and Queenan. In a chaotic sequence, Queenan helps Costigan escape before being thrown to his death by Costello’s crew. A firefight ensues, resulting in casualties on both sides. Enraged by Queenan’s death, Dignam assaults Sullivan and is suspended. Meanwhile, Timothy Delahunt, one of Costello’s wounded men, cryptically reveals to Costigan that he knows he is the mole, before succumbing to his injuries.
Sullivan, combing through Queenan’s belongings, discovers Costello’s double life as an FBI informant. A news report falsely claims Delahunt was a police mole, diverting suspicion. Deciding to eliminate Costello, Sullivan orchestrates a takedown. In the resulting gunfight, most of Costello’s crew are killed. Confronting a wounded Costello, Sullivan learns of his informant status. Betrayed, Sullivan kills Costello, ending their long-standing partnership.
With his mission seemingly complete, Costigan approaches Sullivan to reveal his undercover role, unaware of Sullivan’s true allegiance. However, Costigan notices the same envelope from the theater on Sullivan’s desk, piecing together that Sullivan was Costello’s mole. He escapes before Sullivan can act.
Realizing the danger, Sullivan erases Costigan’s records from police databases, attempting to protect himself. Costigan, meanwhile, visits Madden, who is pregnant, though she has not told him. Suspecting Sullivan may not be the father, Madden takes an envelope from Costigan containing instructions to open it if anything happens to him.
Later, Madden receives a package containing a CD of Costello’s recorded conversations with Sullivan, exposing his treachery. Listening to the recordings, Madden leaves Sullivan. Meanwhile, Costigan arranges a meeting with Sullivan on the rooftop where Queenan died, confronting him and placing him under arrest. Costigan calls Trooper Brown, a fellow academy graduate, for backup. When Brown arrives, he is unsure who to trust and holds both men at gunpoint.
Costigan insists he has evidence linking Sullivan to Costello, persuading Brown to let him proceed. However, as Costigan and Sullivan descend in the elevator, Trooper Barrigan—another of Costello’s moles—shoots Costigan dead in the lobby. Brown arrives but is also killed by Barrigan. To cover his tracks, Sullivan kills Barrigan, framing him as the mole.
At Costigan’s funeral, Sullivan watches as Madden mourns silently. Her reaction confirms their affair. Attempting to reconcile, Sullivan approaches her about the baby, but she coldly ignores him. Shortly after, Sullivan returns home, only to find Dignam waiting for him. Without hesitation, Dignam executes Sullivan, avenging Queenan and Costigan.
As the story closes, the Massachusetts State House looms in the background while a rat scurries across Sullivan’s balcony railing—a symbolic reminder of the deceit and betrayal that defined their lives.
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