The bomber, Alan Dinkler, was unfortunately a victim. Just a pawn in a greater game. He stole $50,000 from his payday loan place of employment and two CDs of client data — names and places they’d sent money to. The amount of cash that he took is quite literally a fraction that was available to him in the vault. Jane, at this point, grows less interested in the way that he does when he’s already on to something else. They find Dinkler’s roommate dead in their house, shot execution style in the had.
While the roommate is collateral damage, Jane is much more interested in the actual motive for the crime. He believes the money was only a cover for what he was really supposed to steal,the CDs of data. He and Lisbon return to the convenience store, where the attendant answers their questions. He claims that Alan had asked for the restroom key, so of course they take it as well. On the wall, they see the graffiti “AD – 297A6 Windsor.” It takes a little searching, but eventually it leads Lisbon and Jane to a locker room in Windsor High School. There, Jane finds Lisbon just as she is waking up, strapped into a bomb just like Dinkler.
After Jane agrees to not pick the lock on the vest, the phone on the shoulder pocket begins to ring. Someone on the other end wants the CDs, which are now in evidence at the CBI . This is used to stall for time while the culprit is found, the attendant.
Jane gets the detonator away from him and Lisbon incapacititates him.. When the rest of the CBI shows up, LaRoche is hauling him in to one of the cars, and Jane and Lisbon argue over the fact that he disobeyed her order to leave. Gunshots go off in the cop car, but LaRoche has emerged the victor. The attendant had picked his way out of cuffs and reached for the gun. He shot in self defense.
The message in the bathroom was a rather clever way of completing his mission — when the attendant blew up Dinkler because he ran into cops, he planted the message there so that it would lead cops to the high school where he could subdue an officer and get them to bring him the CDs. Meanwhile they’ve been running the names on the client list, and they finally get a hit on Max James. Unfortunately, Max James has been found in his home by Rigsby and Cho , dead about four days, gunshot wounds to the knee as well as the head — a torture wound. He is found to have a picture of Madeleine Hightower the team leader on the run.
Jane goes to a hotel room which he describes as “sometimes” living there. Hightower is there, waiting for him, and she is armed. Max James’s death has drawn her out of hiding; they were cousins and he had been sending her money via the payday loan office. It’s become clear that Red John is releasing the dogs of war on Hightower, and he was intending to play for keeps. He asks for forty-eight hours to find Red John’s mole before she turns herself in to police.
First, comes clean with the rest of the team. He and Lisbon meet with Cho, Rigsby, and Grace and they tell them everything, about the enigmatic “Tiger, tiger, burning bright” references by both Red John in last year’s finale as well as by Todd Johnson before he died, the list of four other suspects besides Hightower, and how one of these four people (plus LaRoche) were Red John’s mole. They are all in, and ready to work the case.
Jane approaches LaRoche directly and makes a deal: Hightower for the exchange of the suspect list. At first LaRoche refuses, but Jane begins to make references to LaRoche’s secret, and how Culpepper found a Tupperware container in the vault when he was going through the house. Whatever is in that container, LaRoche certainly doesn’t want people knowing about it, and he hands over the names in exchange for Hightower’s location.
The four names on the list are Brenda (the CBI public relations person), the assistant DA, CBI Director Gale Bertram , and FBI agent Craig O’Loughlin - Grace's fiancé. In a bid to reveal the mole, the team carefully gives the suspected mole access to information about where they are supposedly keeping Hightower, or tells them. The location is a hotel, all rooms on different floors, but right below one another. Whichever room the assassin was sent to would reveal the mole — who would sent the assassin to take out Hightower.
So they set up their cameras in the hotel and lay in wait. When Jane spots the assassin on camera, at first there is skepticism from the team, especially once she gets off the elevator on their floor - the 8th. And they may have been right, except she heads for the stairwell and immediately goes back down, and enters the room that corresponded with Bertram. When they burst in on her, rather than being captured she goes over the balcony’s edge to the pavement below.
With their eye on Bertam as the mole, now, the team as a whole has let down their defenses a bit. Jane takes Bertram to a mall where he says Hightower will be making her surrender, while Cho and Rigsby cover him in any case. Grace is just so relieved that Craig is not the guilty party; so much so that she invites him along to relieve Lisbon on duty guarding Hightower and her children.
About the same time, Bertram realizes he’s been had and informs Jane of the fact. Jane, confident, leads Bertram through the logic: Red John is framing Hightower. Then suddenly in a flash of brilliance, Jane realizes that the rope the assassin had with her would have been used to rappel to the floor below. Red John’s mole is not Bertram, but O’Loughlin.
Having already shot and killed the two members of the Sherriff’s office outside of the gate, Craig is officially a leg up on Grace and Lisbon. When Jane finally manages to get ahold of Lisbon (she was having trouble getting cell service in Hightower's remote safe house) and tell her about Craig, it’s just in time for him to shoot her. Grace and Hightower immediately shoot O'Loughlin while he is distracted by a pillow Lisbon threw at him.
O'Loughlin takes away the necklace he gave to Grace and dies at the cabin. Lisbon is wounded. She gets back on the phone with Jane while Grace calls 911, and he asks her to grab Craig’s phone, hit redial, and tell the person on the other end — who is presumably going to be Red John — that O'Loughlin is dead.
With Lisbon and Jane still on the phone together, he can hear her making the call when the phone on the next table rings. The man sitting there is average. His name is Timothy Carter and seems to be Red John.
Jane sits down with him and they talk. While Red John is well-mannered on the surface, there is a nasty, cold demon lurking beneath. In a tone that is not quite mocking but edges on condescending, Red John informs Jane that he plans to retire from serial murder, and that Jane should give up this revenge business. Jane promises that he will. Once Red John is dead.
To prove he’s Red John, rather than some copy cat or someone sent by the real Red John, he offers that Jane’s wife was rather clean, and smelled like coal tar soap and lavender, while his daughter was sweat and strawberries and cream. Jane starts getting emotional, as it brings back memories, as he attempts to leave, Jane calls him back once more and then proceeds to shoot him in the stomach with a gun that had been concealed in his pocket. Then, while everyone else panics, he sits back down at the table, calmly finishes his tea, and asks the waitress for the check. When the episode ends, Jane has his hands on his head, waiting for his arrest with an eerie calm and sense of peace.