Investigating Susie’s disappearance with Detective Fenerman, Jack believes Susie was murdered by someone she knew. He researches neighbors and eventually suspects Harvey is the killer. Fenerman is unable to find proof, as Harvey has carefully concealed the evidence. Susie’s sister, Lindsey, agrees with Jack’s suspicions, but their casework takes a toll on Abigail. Abigail’s alcoholic mother, Lynn, moves into the house. Feeling alienated from her husband, Abigail goes to California. Susie, in her afterlife, learns that Harvey, who has targeted Lindsey as his next victim, has murdered six other girls, including Holly, and that he stuffed Susie’s body into a large safe in his basement.
One night, Jack, carrying a baseball bat, trails Harvey into the cornfield. However, Jack accidentally stumbles across a teen couple named Clarissa and Brian. Brian, thinking they will be assaulted, bludgeons Jack nearly to death as Harvey watches nearby while Clarissa begs him to stop. As Jack recuperates, Lindsey breaks into Harvey’s house looking for evidence that he killed Susie. Upstairs, she finds a notebook containing a sketch of the underground den, a lock of Susie’s hair, and news articles about Susie’s disappearance. Harvey returns and almost catches Lindsey, but she escapes and rushes home to discover that her mother has returned. She gives the notebook to her grandmother, who contacts the police. Harvey has already fled his home – taking the safe containing Susie’s body with him.
Susie’s afterlife begins expanding into a larger heaven, and she is greeted by Harvey’s other victims. She resists Holly’s urging her to enter Heaven along with the others, claiming she has one final thing to do. Meanwhile, Susie’s classmates Ruth and Ray are present when Harvey drives up to dispose of the safe at a sinkhole dump site on the Conners’ 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 kiss, completing Susie’s last wish, and she returns to Heaven. Meanwhile, Harvey dumps the safe in the sinkhole, leaving it to disappear in the muddy water as he drives away.
Sometime later, Harvey meets a young woman outside a diner and offers her a ride, but she rejects him and leaves. A large icicle falls from an overhead branch, hitting Harvey’s shoulder, causing him to fall backward over a steep 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. 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”.