In 1975, in East Buckingham, a working-class Boston neighborhood beside the Mystic River Bridge, Jimmy Markum, Sean Devine and Dave Boyle play street hockey until their ball rolls down a sewer opening. Jimmy, the more forceful of the boys, then inscribes his name in a square of wet cement in the sidewalk and goads the others to follow suit. The malleable Sean writes his name next, but just as Dave scratches in the first two letters of his name, a black car pulls up carrying two men they assume are policemen. Accusing them of destroying municipal property, one of the men asks where they live. Dave answers that he lives on another street, so the man insists on taking him home, pushes him into the car and slams the door. As the car drives off, the man’s partner eyes Dave, who stares forlornly out the rear window, looking at his friends. Locked in a basement, Dave is sexually abused by the men until he finally escapes four days later, now “damaged goods” as one of the neighborhood men describes him. Twenty-five years later, Dave walks the neighborhood streets with his son Mikey, pointing out the sewer opening that swallowed up hockey balls in his childhood. When Dave glances at the square of sidewalk inscribed with the boys’s names, he remembers his kidnapping and hunches over, crippled by the memory. Jimmy now owns a neighborhood market where he works with his nineteen-year-old daughter Katie, the apple of his eye. The protective Jimmy has forbidden Katie to see Brendan Harris, a neighborhood boy who has been hanging around the store. Sean, now a Massachusetts homicide detective, has left the neighborhood, and one day, while making an arrest with his partner, Whitey Powers, on the Mystic River Bridge, gazes ruefully back at his boyhood home. That night, at McGill’s Tavern, Dave is drinking a beer and watching sports on television when Katie and her friends, Diane Cestra and Eve Pigeon, come in and drunkenly dance on the bar. Dave returns home to his wife Celeste at 3 a.m., shaken and covered in blood, explaining that he bashed a mugger’s head in after the man stabbed him. The following day, an anonymous caller makes a 911 call to police headquarters and states that he found a car spattered with blood in Pen Park in the Buckingham neighborhood. Because Pen Park is under state jurisdiction, Sean and Whitey are called in to investigate. Upon learning that the car was registered to a Katherine Markum, Sean realizes that the victim must be Jimmy’s daughter. Jimmy and his second wife, Annabeth, meanwhile, are in church watching one of their two younger daughters receive her First Communion. After the service, as Jimmy, who is concerned that Katie is not there, is congratulated by friends, a series of police cars race down the street. The sirens are also heard by Celeste, as she scours the newspapers for mention of Dave’s mugger. While walking back to his house, Jimmy passes Pen Park and finds the street cordoned off as a crime scene, then sees Katie’s car. Jimmy, who is accompanied by his thuggish friends, Nick and Val Savage, demands to know what’s going on. Notified of Jimmy’s threatening behavior, Sean leaves the search to try to calm the now smoldering Jimmy. While watching television, Celeste hears the story about the blood soaked car and glances suspiciously out the window at Dave. When Katie’s body is found in the park, Whitey wonders what Sean will say to his friend and Sean proposes “God said you owed him a marker and he came to collect.” After taking Jimmy to the morgue to identify Katie’s body, Sean sits with Whitey, Jimmy and Annabeth in the cafeteria, and Jimmy wonders how their lives would have been different if he or Sean had gotten into the car instead of Dave. Jimmy then recalls that as his beautiful first wife Maria was dying of cancer, he was serving a two-year stint in prison for robbery. When Jimmy mentions that Brendan and his mute brother Silent Ray came looking for Katie the morning of her disappearance, Whitey remembers finding travel brochures for Las Vegas in the back of Katie’s car and wonders if there might be a connection. Later, Sean’s estranged wife Lauren, who left him when she was pregnant, calls Sean from a payphone but won’t speak. As mourners gather at the Markum house, Dave sits zombie-like while Celeste, who is Annabeth’s cousin, watches and wonders if he might be involved in Katie’s death. Meanwhile, Sean and Whitey question an old woman who lives across from Pen Park. When the woman states that after Katie’s car squealed to a stop, she heard Katie say hello to someone, the detectives realize that Katie knew her killer. Sean and Whitey then go to question Eve and Diane, who admit that Katie and Brendan planned to elope to Las Vegas. When the detectives go to the Harris house to tell Brendan about Katie’s murder, Brendan’s shrewish mother Esther expresses pleasure, exclaiming that Katie was “no good.” Esther then undermines Brendan’s alibi that he was at home at the time of the murder. At the Markum house, a troubled Dave walks out onto the porch and finds the brooding Jimmy. When Jimmy asks about Dave’s injured hand, Dave says that he slammed it in a door. Suddenly breaking down, Jimmy sobs that when he returned from prison, he felt like Katie and he were the only two people on earth. Later that night, Sean is at home thumbing through some old photos of Dave, Jimmy and himself when Lauren calls. He begins to talk about work, but when she does not speak hangs up, saying he "can't take it tonight." Meanwhile, Dave tells Mikey a bedtime story of a boy living in a world that others never saw, as he thinks of his kidnapping. Celeste interrupts by calling Dave to the stairway, and when she wonders aloud why the newspapers still have not printed a story about the mugger, Dave menacingly advances toward her. Later, as Jimmy gazes out his bedroom window, he muses that he is in some way responsible for Katie's death. After Brendan passes a polygraph test, Sean and Whitey decide to question Dave. Under Whitey’s interrogation, Dave admits to what Sean and Whitey already knew, that he saw Katie at McGill’s on the night of the murder. Afterward, Whitey, who has noticed Dave’s injured hand, tells Sean that he thinks Dave is the murderer. At the funeral home, Jimmy stands over his daughter’s body and vows to avenge her killing. Later, when Sean tells Jimmy that Katie was planning to elope with Brendan, Jimmy voices his contempt for Brendan’s father Ray because he ran off and left his family. Impatient with the slow pace of the investigation, Jimmy then gives Sean a deadline, after which he says, he and his pals the Savage brothers will conduct their own inquisition. When ballistics determine that the gun that shot Katie was also used in a liquor store holdup eighteen years earlier, Sean and Whitey go to question the liquor store owner, who suspects Ray Harris of the robbery because Ray had once worked at the store and therefore had a key to gain entry. Meanwhile, after sitting alone in her car in the pouring rain, Celeste returns home and finds Dave transfixed in front of the television watching a vampire film. After explaining that he is fascinated by vampires because “if you are undead, it’s okay to forget to be human,” Dave asks Celeste if she thinks he killed Katie. When Celeste hesitates, Dave breaks down and, referring to the past, states that to survive, he had to pretend to be someone else and that Dave died in the basement. Unstrung, Dave goes out for a walk, and when he passes Jimmy on the street, admits that he saw Katie on the night of the murder. Later, as Jimmy is picking out a gravestone, the Savage brothers drive up and inform him that the police have brought Dave in for questioning. After releasing Dave, Sean and Whitey look into the robbery. They discover that, although Jimmy and Ray were both arrested for the liquor store robbery, only Jimmy served time, and realize that Ray must have made a deal to turn in Jimmy. Because Ray disappeared shortly after Jimmy left prison, the detectives ask Brendan about his father’s gun. Although Brendan reveals that his father sends the family $500 monthly, he becomes defiant when told that Ray’s gun killed Katie and denies that his father owned a gun. At the same time, a shaken Celeste confides to Jimmy that Dave returned home on the night of the murder covered with blood. When Jimmy asks Celeste if she thinks Dave killed Katie, she nods her head yes. Soon after, Dave is walking down the street when the Savage brothers, who are also Celeste’s cousins, drive by and invite him to go drinking. Dave climbs into the car’s backseat and looks forlornly out the rear window as they drive to the Black Emerald Bar at the edge of the Mystic River. At police headquarters, Sean and Whitey realize that they have not listened to the 911 tape, and upon playing it, are astounded when a boy’s voice, claiming that he did not see the murder, nonetheless identifies the victim as a woman. As the Savage brothers ply Dave with drinks at the bar, Jimmy, mad with grief and rage, joins them. Sickened by the alcohol, Dave runs out the back stairs to vomit, and while standing over him, Jimmy reveals that he killed Ray not for turning him in, but because going to prison meant that he could not take care of Maria when she was dying. Aware that Jimmy now thinks he killed Katie, Dave swears that he killed a child molester that night, not Katie. Exploding in a rage, Jimmy demands that Dave confess to Katie’s murder and offers to release him if he does. Meanwhile, at the Harris apartment, Brendan has discovered that his father’s gun has been removed from its hiding place and waits for Silent Ray to return. When Ray and his friend, John O’Shea arrive, Brendan shows his brother the empty holster and orders him to speak. After John tries to defend his friend, Brendan kicks him in the face, then lunges for his brother’s throat. Just as John aims the gun at Brendan, Whitey and Sean burst in and grab the gun. At the Black Emerald, Dave, certain that Jimmy will kill him unless he confesses, admits to killing Katie, then remarks that she reminded him of the youth he never had. Dave tells Jimmy “you’d know what it meant if you got in the car instead of me.” Jimmy then plunges a knife into Dave’s stomach, then shoots him. Soon after, Jimmy is sitting hunched over on a neighborhood curb when Sean pulls up and informs him that they caught the killers, Silent Ray and John. Stunned, Jimmy asks if they are certain, after which Sean explains that the boys were playing in the street when the gun went off by mistake, hitting Katie’s car. Afraid that Katie might tell someone, the boys chased her down, shot and beat her. Sean then asks if Jimmy has heard from Dave, explaining that he needs to talk to him about a body of a pedophile that has been found. Sensing that Jimmy might have killed Dave, Sean asks when he saw Dave last, to which Jimmy replies “twenty-five years ago.” Sean then inquires if Jimmy is going to send monthly checks to Celeste as he has done for the Harris family, and says that he wishes that they were still eleven-year-old boys and that it all was just a dream. Soon after, Sean’s phone rings, and intuiting that it is Lauren, he says that he is sorry he pushed her away. Emboldened, Lauren speaks, admitting that she is sorry, too, and agrees to come home with their baby. Some time later, as the neighborhood celebrates Columbus Day with a parade, Jimmy watches from his window and confesses to the steely Annabeth that he killed Dave and threw his body into the Mystic River. Annabeth consoles her husband by saying that he is a king and everyone is weak but him, then makes love to him. On the street, Celeste threads her way through the crowd, but upon spotting Sean and his family, turns away. As the float on which Mikey is riding passes by, Mikey morosely stares off into space. Jimmy then comes out onto the street and smiles at Sean, who forms his fingers into the shape of a gun and fires at him.