When a prosecutor, Mark Hastings, reappears after missing for 12 years, Red suspects that he was being held and punished by "The Judge," who punishes those who misappropriate justice.
Liz's investigation leads her to Frank Gordon, who had his conviction overturned and works in a book depository for prisoners. Liz and Ressler go to question Frank, but he attacks Ressler and escapes. They find letters from convicts and information about a prisoner set to be executed the next day.
Liz investigates and finds that Cooper was the one who got the confession of out him. It turns out that he beat the prisoner, Allan Ray Rifkin, for a confession under the orders of Connelley. She questions Cooper about it, but is warned off it. She finds proof that Cooper did beat a confession, but isn't able to stop the execution.
Both Cooper and Connelley were were taken by The Judge. They were found guilty and Cooper was about to be executed, but the FBI showed in time. Red uncovers proof that Rifkin was guilty despite being beat. He shows Ruth the proof and reminds her that she's about getting justice. She turns herself in and all the prisoners are freed.
Tom's at his teacher's conference in Orlando and Jolene tries to seduce him. She gives him a key and he shows up to tell her he loves Liz. Jolene tells him he doesn't that he's on the job. He admits to marrying her as part of a job, but hadn't heard anything in two years from his handlers.