One year on from the Season 2 ending and Joe Caroll is on Death Row facing execution. Ryan is attempting to move on with his life and is in a relationship with a woman named Gwen. When the FBI discover three bodies in a hotel room with a message that says 'Ryan Hardy Lies', he learns that Mark Gray has re-emerged. Concerned for Gwen's safety, Ryan attempts to break off their relationship but she refuses. They learn that Mark now has followers and that they are recreating the scenes in which Mark
Mark's followers abduct the FBI Agent Jeffrey Clarke and attempt to kill his wife Anna; Mark then makes contact with the FBI and gives them a deadline of 8 p.m. to tell the truth about what happened to Lily Gray. Rather than visit Joe in prison, Ryan visits Dr. Arthur Strauss to learn more about Andrew and his motives. When Jeffrey escapes from Mark's followers, he makes contact with Ryan and the FBI trace the call to Reading, Pennsylvania. Now recaptured, Jeffrey is forced to make a confession
Ryan attends a press conference to deny the allegations made by Clarke. He explains to the reporters that Clarke's confession was made under duress and that Mark Gray and his followers were responsible for his death. Kyle and Daisy have their doubts about remaining with Mark when Ryan reveals a sketch of them to the press and reaches out to them to make contact. Kyle and Daisy meet with Julianna, who tells them to stay with Mark and gives them a file on Max Hardy, which contains her address and
Mark and his followers attack a fire station, killing the people inside. The next day, Daisy and Kyle inadvertently lead the FBI to Mark when they're caught on camera; Mark evades capture and desperately calls Daisy, who ignores his calls, leaving Mark suspicious that Daisy was helping the FBI. After investigating the house, Ryan, Max and Weston realize that Daisy and Kyle's next target is the daughter of a judge involved in the Strauss trial. They make their way to the campus to find that Kyle
Ryan works out that all the events thus far were solely aimed at discrediting the FBI in order to influence the outcome of Strauss' trial. Daisy and an injured Kyle are reunited with Mark but their main focus is to safely escape from him. Mark realizes that Kyle and Daisy have just been using him. Kyle and Daisy's next target is the journalist Carrie Cooke, who is a key witness at the trial. Carrie is kidnapped and killed, which results in the case against Strauss being dismissed. The FBI catch
Ryan visits Joe Carroll in prison to ask him to help find Arthur Strauss. Joe agrees to help only if Ryan will agree to visit him regularly until his execution. Joe suggests that they look into Strauss' former pupils and any he may go to for help. The FBI find themselves in Beacon, NY where there has been an unusually high number of missing persons. The local sheriff isn't interested in helping the team. However, the deputy is far more welcoming. In the meantime, Strauss is hiding in a cabin in
There is a week remaining until Carroll's execution and Ryan visits him again hoping to learn who Strauss' 'favorite student' was. Joe tells him that Strauss kept all his students isolated from one another in order to keep them dependent on him; with few exceptions, the killers don't know who each other are. Theo rescues Duncan Banks, killing two US Marshals in the process. The FBI trace the fake passports they found on Strauss to a government employee, Luis, but Theo and Duncan want to get to L
Mike and Ryan begin working on finding Theo only to be stopped by Donovan. After finding a house with Theo's stuff, they learn he is still out there. A friend of Theo's wife invites them to a party only for Theo's wife's friend to reveal she is aware of some of Theo's activities. This causes Theo to kill her and her husband. Joe invites Ryan to his execution only to be rejected. After discovering the murder, Ryan and Mike discover Theo's location and real name through his wife. However, Theo dis
Ryan and Theo are both led back to Joe for different reasons. Joe promises Ryan information about Theo but the latter refuses to talk to him. Theo recruits a former soldier to talk to Joe about some information on some codes he has, but Joe kills the soldier and secretly takes his sunglasses. Elsewhere, Max and Weston trace the stolen laptop, but it is destroyed by Tom. Mark, now having a dual personality with "Luke" as his guidance, closes in on Daisy. They reach a compromise to use her laptop
It's Joe Carroll's execution day and Ryan is determined to free himself. Using the sunglasses he has fashioned into a weapon, Joe kills his guards and takes three hostages. He addresses the horrified FBI and demands that Ryan comes to him or the hostages will be killed. Ryan persuades Joe to let one hostage go before he is handcuffed and tazered. Meanwhile, Theo brings his sister to the apartment and briefs her on the situation. He hacks into the prison's security network and watches Joe and Rya
Ryan feels the aftereffects of his late night drinking of having slept with a random woman. He confesses this to Gwen, who leaves him knowing how unstable he has become. He drinks to drown his sorrows. Theo and Penny visit a wealthy yet sadistic resort for killing; the head of which, Eliza, can help them escape but only if Theo kills Ryan. Ryan works together with agent Lisa Campbell to dig into Theo's past and learn that, as a 10 year old, he had someone murder his family. They track the killer
Theo goes to meet Daisy and Mark, who reveal there is a corrupt FBI agent on the inside and that they intend to work together. Theo agrees but only on his terms. He goes to meet with Eliza, who has ordered a hit on him but Theo kills her men. Ryan and the team work on the recent information and discover a location that may be a hiding spot for Theo and Sophia. Meanwhile, Tom tries to get rid of all evidence of the cameras in Max's apartment and the dead body of agent Sloan, only to be caught by
Ryan agrees to Theo's trade and brings Max up to date on his actions. The FBI find their location and learn of Tom's betrayal. Mike attempts to escape, but is cornered by Mark. Not trusting him anymore, Daisy shoots Mark in his shoulder and he flees. Theo has the trade take place at a theater intending to kill them all but Max stops Daisy. As they make their escape, Penny refuses to leave without making Ryan pay. She goes back to kill him but is killed herself in the process; Theo manages to esc
Mike is rushed to the hospital where he undergoes surgery. Gwen is called for protection upon Ryan's request and gives him her ultrasound. Theo talks with Eliza, who promises him a way to leave the country when Ryan is dead. Ryan briefly meets Eliza at her hotel, after which she becomes paranoid and requests that Ryan be kept alive. Theo and Daisy kidnap Mendez and her family, forcing Ryan to meet him. Knowing of the trap, Ryan sets up a perimeter around the house. Mendez escapes with her spouse
After torturing Ryan, Theo kills Agent Barton for payback against Sophia. Mike awakens at the hospital and Max informs Lisa of Theo's location, who is revealed to be a mole for Eliza. Max and Lisa follow Theo's trail, only to find a dead end. Eliza finds Theo and has her men torture him, while she interrogates Ryan on what he knows about her. While the latter knows nothing of her, she doesn't believe him and threatens to kill everyone he knows. Ryan and Theo escape, to which Theo learns of Gwen'