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 husband. Jane quickly deduces that the husband was the killer, and tricks him into taking Jane hostage. Jane had secretly disabled the mans gun, and casually invited SacPD Officers to come and arrest the man. However, the athlete pulls out a second weapon and kills an officer when they let their guard down.
This incident leads Gale Bertram to push Jane and Lisbon to leave the city, taking on a case in Mexicali. Lisbon believes this is a ploy by Bertram to get them away from the city; however, Jane is not as worried. Lisbon shares Jane's list with Van Pelt, which leads to the whole team knowing. However, Lisbon and Jane argues 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, Lisbon pursues a lead on her own. This leads her to an abandoned house where she finds Brett Partridge, near death. Shortly before dying, Partidge 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 last scene is a shot of Lisbon lying down, status unknown, with an unknown person drawing a Red John smiley face on Lisbon's face in blood.
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