"Gone Baby Gone" is a film based on the best-selling Dennis Lehane novel of the same name. The story revolves around P.I. Patrick Kenzie (Casey Affleck) and his girlfriend Angie Gennaro (Michelle Monaghan) who are contacted by the relatives of a missing girl from the Dorchester neighborhood of Boston. Initially reluctant to take the case, after meeting with the girl's mother and police Captain Jack Doyle (Morgan Freeman), they decide to join the search for the child. Patrick begins by questioning many of his old acquaintances as well as consulting with detectives Remy Bressant (Ed Harris) and Nick Poole (John Ashton).
The girl's mother, Helene, worked as a mule for a local drug lord and during a botched delivery her boyfriend stole money. It is believed that the drug lord has taken the child as collateral for the money, an exchange is set up near a quarry but after a short firefight it is believed that the child drowned in the quarry.
Patrick moves onto the next case in which another abducted child has been taken by a convicted child molestor. Patrick, with the help of Remy and Nick, kills the molestor but the boy has already died and Nick was severely wounded by gunfire; he eventually dies of his wounds.
As time passes and after conversations with police officers, Patrick begins to realize the missing girl case was fabricated and that the child's uncle conspired with Remy to save the girl from her mother. Remy tries to cover his tracks later on by staging a robbery in a bar but is shot twice and dies after fleeing. Further questioning makes Patrick realize that Captain Doyle was also involved and has taken the child as his own.
Patrick struggles with what to do, knowing that the child is better off with Doyle, but ultimately reports it to the police. The final scene reveals that the mother has continued her neglectful ways, leaving her alone without a babysitter.