Jane and the team are back to work and all charges from the end of last season have been dropped as the CBI and FBI both attempt to cover up Jane's unsuccessful take down of Red John and Wainwright's death. This doesn't sit well with FBI field agents Mancini and Smith, who show up at the CBI's first crime scene and attempt to take over the case. Despite the teams almost coming to blows, re-instated CBI director Gale Bertram tells everyone that they have to get along for the sake of the cover-up. Of course, Jane isn't much for taking orders, nor is he happy when the FBI announces that they want custody of Lorelei Martins, the Red John disciple who Jane believes is the key to finally capturing the elusive killer.
Meanwhile, the team attempts to solve the murder of two retail workers - a man and a woman - whose bodies are found in a Sacramento apartment. While the victims were co-workers, they didn't seem to be lovers or even friends. While Jane misdirects the FBI into pursuing a dead end, he and the team investigate how the victims were connected.