Part 1: The Boys Who Escaped From Wolves (1975)
Mystic River opens in 1975 and introduces three young boys who are ten and eleven years old and live in East Buckingham, a working-class part of Boston. Two of the boys, Jimmy Marcus and Dave Boyle, live in the Flats area, while Sean Devine lives in the nicer Point area. Sean's father works as a foreman in a candy factory, where Jimmy's father is also employed. Dave tags along wherever Jimmy goes, including the Saturday visits that Jimmy and his father make to Sean and his father.
After an incident where Jimmy, the daredevil of the group, jumps onto the subway tracks to retrieve a lost ball and has to be dragged off the tracks,Sean's father tells Sean he can only play with Jimmy in front of their home. The next time Jimmy and Dave visit Sean's house, Jimmy is not as exuberant. His father has lost his job. Dave tries to lighten the mood by telling a joke, but his efforts are ignored by the other two.
Jimmy suggests they find a car with its keys under the seat and take it for a joyride. He asks Sean which cars on the block would be best to take, but internally Sean does not like this idea. He suggests to Jimmy that they do this some other time. Dave punches Sean in the arm for his suggestion, and Sean punches him back, hard. Sean and Jimmy get into a physical confrontation.
As Sean and Jimmy are fighting, a car, "square and long like the kind police detectives drove," stops near them. The driver, who looks "like a cop," gets out and asks the boys where they live. Jimmy lies and says he lives in the neighborhood, but Dave tells him that he is from the Flats. The man insists that Dave get in the car with them, warns the boys about fighting, and tells them that Dave will be taken home to his mother.
After the car leaves, Sean's father learns of the incident and immediately realizing that it is a kidnapping, calls the police. The men in the car were not police officers, but kidnappers. Sean feels guilty about not getting in the car and wonders what has happened to Dave. Jimmy feels resentful of Sean and does not believe he will ever see Dave again. Apparently, the kidnappers leave Dave alone at one point and he escapes. Four days after his abduction, Dave is found alive. His neighborhood is overjoyed at his return and throws a block party. Dave looks shell-shocked and withdrawn. Seeing him at the party, Jimmy knows that something has changed in Dave.
Though Dave initially receives support from his neighbors, his classmates harass him when he returns to school. He does not fully understand what happened to him, especially why the men picked him and not Sean or Jimmy. He relives part of the experience and tries to come to terms with what happened to him.
As they grow up, Jimmy and Dave no longer see each other very much. Jimmy steals a car and is sent to another school. Meanwhile, Sean cannot stop dreaming about the experience. One year after the incident, he learns that one of the men who abducted Dave has been caught and killed himself. Before his suicide, the man reports that the other kidnapper died in a car accident the previous year.
Part 2: Sad-Eyed Sinatras (2000)
It is now twenty-five years later and Brendan Harris, the secret boyfriend of Jimmy's nineteen-year-old daughter Katie, is preparing for the couple's elopement to Las Vegas the next day. Brendan's preparations and hopes for life are contrasted with background about Jimmy's life since that fateful day in 1975. Jimmy still lives in the Flats. He has served time in prison, during which his first wife, Marita, died of skin cancer, leaving him a single father. He later remarries and has two more daughters. After serving his time, he leaves his life of crime behind for Katie's sake.
That same night, Dave, who also still lives in the Flats, is preparing for a night out. His wife, Celeste, is having her girlfriends from work over to watch the movie Stepmom, while their young son Michael sleeps in his room. As Dave walks to a local bar, he worries about having to move away from the neighborhood. Yuppies and college students have been moving into the area, raising property values and rents.
Katie goes out with her best friends, Diane Cestra and Eve Pigeon, to celebrate her impending marriage. They go to dinner, then to a number of bars. Dave's evening intersects with Katie and her friends. He watches the Boston Red Sox baseball game at the same bar where Katie and her friends drink and dance on the bar top. After a night of drinking, Katie drops off her friends at Eve's house. As she drives home, she hits something in the street and stops the car. Someone familiar approaches the car, but he is armed with a gun.
Meanwhile, when Dave returns home to Celeste, he is cut across the chest, has an injured hand, and is bleeding profusely. Dave tells Celeste that he was mugged, and he beat the attacker so badly that he might have killed him. Celeste does not believe his story, but still takes care of him, agreeing not to call the police or take him to a hospital. She immediately washes Dave's bloody clothes and plans to destroy all evidence from Dave's attack. Though she is scared of what has happened, she is protective and fiercely loyal to Dave.
The next morning, Jimmy learns that Katie has not shown up for her Sunday morning shift at the Cottage Market, the corner store he owns. Jimmy is especially tense because it is the morning of the first communion of his youngest daughter, Nadine. As he dresses to go into the store, his wife Annabeth is annoyed that her stepdaughter has created tension on Nadine's special day. Jimmy reflects on the loss of his first wife and his early days with Katie when he was unsure how to be a father. While Jimmy covers Katie's shift at the store, he makes calls to try and find her. Brendan drops by the store with his younger brother, a mute named Ray, and tries to learn where Katie is without attracting suspicion. Jimmy does not like Brendan and has forbidden his daughter from ever seeing him.
Sean re-enters the narrative as a state trooper working homicide after a week-long suspension. His personal life is in disarray because his wife, Lauren, has left him. He is put on a case after two kids call 911 to report a car covered in blood near Penitentiary Park in the Flats. At the scene, Sean meets with his partner, Whitey Powers, a veteran in homicide. Though a body has not yet been found, the authorities assume from the blood in the vehicle that the victim has been murdered.
During and after Nadine's communion service, Jimmy is angry that Katie has not shown up, but he is also worried. He reflects on his past again, revealing that he was a very clever criminal who had his own crew. He went to prison to protect the others in his gang.
When Celeste wakes up on Sunday morning, she is still worried about what actually happened to her husband the previous evening. She is certain he lied to her about the incident. She knows something happened to her husband as a child, but he has never told her exactly what the experience was. The tension increases between Celeste and Dave.
Jimmy, on a hunch, follows the police cars to the area where the car has been found. When he sees that Katie's car is involved, he knows in his heart that she is dead. Jimmy asks to see Sean, who is reluctant to talk to him. When they meet, Sean informs him that she has not been found yet, but Jimmy cannot accept that answer. Rather than wait on the police, Jimmy decides to find his daughter on his own.
The police find Katie's body behind an old drive-in movie theater screen in the middle of the park. She has been shot in the head and beaten. As Sean surveys the location, Jimmy and his brother-in-law, Chuck, enter the park through a back entrance and approach the murder scene. Jimmy learns that his daughter is dead. Sean and Whitey are the lead investigators of the crime.
After Jimmy identifies Katie's body at the morgue, Sean and Whitey question him and Annabeth. Jimmy brings up what might have happened if he and Sean had gotten into the car with Dave. Though internally Sean reflects on the fact that he has asked himself the same question over the years, he keeps focus on the case at hand. As Whitey and Sean begin their investigation, Sean tells him what happened with Dave all those years ago.