In 1973, Susie Salmon , a 14-year-old girl living in Pennsylvania with her parents, sister, and brother, dreams about becoming a photographer some day. One day, Ray Singh , a boy Susie has a crush on, approaches her at her locker and slips a note into her textbook. He asks her out for the following Saturday. As Susie walks home through a cornfield, she runs into her neighbor, George Harvey , who coaxes her into an underground den that he says he has built for the neighborhood children. Inside, Susie becomes uncomfortable in Harvey's presence and attempts to leave; when he grabs her, she kicks him in the face and runs into the field and onto the street, rushing past Ruth Connors , a fellow classmate.
Meanwhile, the Salmon family becomes worried when Susie does not return home. Her father, Jack , leaves to search for her, while her mother, Abigail , waits for the police. In town, Susie sees her father, but he does not respond to her. Susie then runs home to find Harvey soaking in a bathtub. After seeing her charm bracelet hanging on the sink faucet near a bloody shaving razor, Susie realizes that she never escaped the den and was actually murdered by Harvey. Screaming, she is pulled into the "In-Between", that is neither Heaven nor Earth. From there, Susie watches over her loved ones, unable to let go despite her new afterlife friend, Holly , urging her to move on.
Investigating Susie's disappearance, Detective Len Fenerman thinks that Susie was murdered by someone she knew. Jack begins obsessively researching neighbors, including Harvey, whom he comes to think is the killer. Fenerman interviews Harvey but is unable to find any evidence that would link him as a suspect. Susie's sister, Lindsey , comes to agree with her father's suspicions, but their casework takes an emotional toll on Abigail, and Jack invites her alcoholic mother, Lynn , to move in with the family. Feeling alienated from her husband, Abigail leaves for California. In her afterlife, Susie inspects a lighthouse and learns that Harvey, who has now targeted Lindsey as his next victim, has murdered six other females, including Holly, and that he stuffed Susie's body into a safe in his basement.
One night, Jack, carrying a bat, trails Harvey into the cornfield. However, Jack accidentally stumbles across Susie's friend, Clarissa . Her boyfriend, Brian , who mistakenly thinks that his girlfriend is being assaulted, nearly beats Jack to death while Harvey watches from a hiding spot. As Jack recuperates, Lindsey breaks into Harvey's house looking for evidence. Upstairs, she finds a notebook containing a sketch of the den, a lock of Susie's hair, and news articles about Susie's disappearance. However, Harvey returns home and hears Lindsey, who barely escapes and runs home to discover that her mother has returned. Not wishing to spoil the happy reunion of her parents, she hides the book from them and instead gives it to her grandmother. Fearful of being caught, Harvey flees, taking the safe with Susie's remains with him.
The realm in Susie's afterlife begins expanding into a larger heaven, and she is greeted by Harvey's other victims. She resists Holly's urging to enter heaven along with the others, claiming she has one final thing to do. Meanwhile, Ruth and Ray are present when Harvey drives up to dispose of the safe at a sinkhole dump site on the Connors property. Susie returns to Earth and enters Ruth's body, causing Ruth to faint. Ray rushes to Ruth's aid only to realize she has become Susie. They share a kiss, completing Susie's last wish, and she returns to Heaven, as Harvey drives away. Meanwhile, the safe is seen tumbling down the sinkhole before disappearing into the muddy water.
Sometime later, Harvey meets a young woman outside a diner and offers her a ride, but she rebuffs him and leaves. A large icicle falls from an overhead branch, hitting Harvey on the shoulder. He loses his balance on the ice and falls backward over a cliff to his death. Time passes, and Susie sees that her family is healing, which Susie refers to as "the lovely bones" that grew around her absence. As the film concludes, Susie finally enters Heaven, telling the audience: "My name is Salmon, like the fish; first name Susie. I was 14 years old when I was murdered on December 6, 1973. I was here for a moment and then I was gone. I wish you all a long and happy life."