Hodgins is experiencing neuropathic pain as the feeling returns to his legs. It causes intense leg cramps that he can’t control. 

Brennan has nightmares about the “The Puppeteer” serial killer as who has killed another victim and left her covered in rats in an classroom like setting of an abandoned building. 

The victim, Melissa Goodman, is wearing an outfit that Brennan donated to a women’s mission center. He also styled her hair to make her look like Brennan and fed the victim Brennan’s favorite.

Brennan tells her father that she’s been feeling as though someone is following her. Melissa Goodman’s psychiatrist, Dr. Brandon Faulk says she was paranoid and also having nightmares. 

Hodgins thinks that the killer is planting evidence in order to mislead the investigation. Aubrey figures out the the children’s songs on a the mix tape all came from a book of children’s songs published in 1978 in Michigan. 

Somewhere, the killer makes puppets and is surrounded by cut out photo heads of everyone close to Brennan.  

Aubrey gets a lead on Graham Reynolds, who owns a puppet store and spent two years in prison for attempted murder. They arrest him when he tries to escape and they find a puppet made up to look like Brennan and photos of those close to her. Turns out that someone was subletting his basement for the last year but he doesn’t know his name. 

Brennan continues to have horrifying nightmares and decides to see Dr. Faulk for help. Booth figures out that the one connection between Melissa Goodman and Brennan is Dr. Faulk. He runs in to Brennan’s session and arrest Dr. Faulk but Brennan doesn’t believe he’s the killer.

Brennan heads back to the lab and wonders why no one else is there. Someone sent an email from her address to the rest of the crew telling them to meet her at the Founding Fathers. Brennan is abducted from the lab.

Booth, Aubrey and the team at the lab construct a murder board too look at all of the information about the killer as well as the notes from Brennan’s session with Dr. Faulk, who believed she was remembering something connected to the killer. When they put all of the clues together (weak/burnt hands, someone who knows anatomy and robotics, etc.), it sends Booth running out of the building. 

Booth goes to the mental health facility and finds that Zack has escaped. Somewhere Zack is holding Brennan. He tells her they have a lot to catch up on.