The central twist of "Prisoners" is the revelation that Holly Jones (Melissa Leo), the seemingly harmless aunt of the initial suspect Alex Jones, is the true kidnapper. Her motivation is a twisted "war on God," born from the trauma of losing her son to cancer years ago. She and her late husband began abducting children to cause parents to lose their religious faith, turning them into vengeful "demons" like themselves.
Several key plot points are re-contextualized by this reveal. Alex Jones is not a perpetrator but was Holly's first-ever victim, and his mental state is a result of childhood trauma. His cryptic statement, "They didn't cry 'til I left them," was not a confession but a fragmented memory of him leaving the girls with Holly. The other major suspect, Bob Taylor, who had the bloody children's clothes and maze drawings, was also a former victim of the Joneses. His actions were a form of traumatic reenactment, not an original crime.
The mummified corpse found in the basement of the priest is Holly's husband. He confessed his sins to the priest years ago, admitting to killing 16 children, which led the priest to murder him and hide his body. The maze symbol, which connects all the victims, was an obsession of Holly's husband, a symbol he passed on to his traumatized captives.
The ending sees Keller Dover, after realizing Holly is the culprit, getting trapped in a hidden pit in her yard where she kept the children. Detective Loki, piecing together the maze necklace clue, arrives at the house, kills Holly in a shootout, and rescues Anna. In the final scene, as the police are wrapping up the crime scene, Loki faintly hears Keller blowing Anna's lost whistle from beneath a parked car, leaving his rescue ambiguous but heavily implied.