Jane and Lisbon secretly continue their dangerous mission to narrow down the list of seven Red John suspects as they investigate the murder of a man who was missing for two years.
Following the events of the Season 5 finale, Lisbon and Jane are called to a crime scene, where a woman is found dead by her baseball player fiancée, Jane quickly deduces that the husband was the killer and tricks him into taking Jane hostage. Jane had secretly disabled the man's gun. He casually invites SacPD Officers to come and arrest the man. However, the athlete pulls out a second weapon, shooting and possibly killing (it's never stated clearly) an officer when they let their guard down. SacPD is understandably enraged with the display of arrogance that make a bad situation worse.
This incident leads Gale Bertram to push Jane and Lisbon to leave the city, taking on a case in Salton Sea State Recreation Area where a body has been found buried in the desert. Lisbon believes this is a ploy by Bertram to get them away from the city; Jane is not as worried which leads Lisbon to think Jane is overwhelmed and unsure what to do next. In an effort to do something constructive, Lisbon shares Jane's list with Van Pelt, instructing her to place tracking bugs on the phones of the seven suspects. The revelation and the order upsets Van Pelt. Rigsby asks her what's going on and is suspicious of her evasive answer. Later, while waiting to interview the wife of their current case victim, Cho is bothered by Rigsby's awkward behavior and asks what's bothering him. It's later revealed that the whole team knows about the list of seven and the fact that Red John knows too. Lisbon and Jane argue over this and she leaves, heading back to Sacramento. The case is solved with Jane's usual prowess, as he quickly deduces that the three employees of the diner had killed the man for money.
Following an anonymous tip about a state officer in danger, Lisbon realizes that the address provided in the tip is the same address where Van Pelt's tracking program shows Brett Partridge is. This leads her to a closed-up, condemned house where she calls for backup by SacPD. Before it arrives, she hears a noise in the house and goes inside. The house appears abandoned but further exploration leads her to a bedroom where she finds Partridge near death. Shortly before dying, the forensics tech whispers "Tyger, Tyger" to Lisbon, an allusion to the poem recited to Jane by Red John at the end of Season 2. After turning around she sees a door that is now open, which was closed moments earlier. As the scene fades, Lisbon is seen jerked backwards by an off-screen assailant. Back at the station, Jane gets a call, presumably from Lisbon, but "Red John's voice" tells Jane that Lisbon "Can't come to the phone." The caller is shown wiping blood from a linoleum knife, Red John's preferred implement for cutting and killing. The last scene is a shot of Lisbon lying down, status unknown, as a Red John smiley is drawn with blood upon Lisbon's pale face.
- Jane's List of Suspects narrows to six after Brett Partridge is murdered by Red John.