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A year after he was convicted of killing a young woman, a prisoner called Jared Renfrew contacts Jane offering information on notorious serial killer Red John. Unable to resist the temptation to find the man who killed his wife and child, Jane visits Renfrew in jail to hear his story. The convict claims that he did not kill the girl and will provide "dynamite information" if Jane helps him prove his innocence. "You get me out of here and I'll give you Red John," he says. To support his claims, he reveals information about the murder of Jane's wife that was never released by police.
Despite warnings from Minelli to leave the case alone, Jane visits the mansion of the wealthy Renfrew family to poke around. However, he is forced to leave the property when Jared's powerful brother, Gardner, calls the police. Back at HQ, Minelli has found out about Jane's actions and is furious. "If you pursue this any further, I'm going to have to throw you out of the CBI," he spits. "I don't want to have to do that." But Jane is undeterred. "I'll spare you the trouble," he says, handing Minelli his badge. "I quit." Faced with suspension for supporting Jane, Lisbon and the other agents stand firm and are eventually given a week's grace to carry out a sub-rosa investigation of the Renfrew case with Jane.
While carrying out some research on the police computer network, Van Pelt receives an instant message reading 'keep up the good work' from a user in New Hampshire with the tag Dr Joe, NH. To everyone's horror, Jane reorganises the letters on screen to form the name Red John, but the agents are unable to trace the message. "He somehow tapped into the secure network," says Van Pelt. "He's been spying on us!" "He wants us to succeed - he wants Renfrew out of jail," concludes Jane. "That way he can get at him to silence him," adds Rigsby. Now convinced that Jared really does have information on Red John, Jane and Lisbon redouble their efforts to cast doubt on his conviction.
Before long, they have discovered that one of the witnesses in Jared's trial was paid to lie. Moreover, Jane is able to discredit some of the physical evidence used to send Jared to prison. In light of these developments, Jared's conviction is overturned and he is released from jail. A jubilant Jane picks him up with the other agents and drives him back to HQ. However, while the car is caught in traffic, Jared escapes and flees into the crowded streets. Jane and Rigsby give chase, but they lose sight of their man.
With the one man who can reveal Red John's true identity now missing, Jane may never find his wife's killer. But the consultant is given hope when Jared calls the station to apologise for reneging on his end of the deal. "It was dishonourable, I know, but crossing Red John just seems too dangerous," says Jared. "You've already crossed him - you need our protection," retorts Jane, but Jared hangs up. The call is traced to Tijuana, Mexico. "This isn't over," says Lisbon. "We're gonna find Renfrew and he's gonna tell us what he knows." Can the agents get to Jared before Red John finds him and silences him forever?