Season synopsis
Contains spoilers for this season and earlier seasons.
Six months after Booth and Brennan leave the FBI and Jeffersonian, they are living with their children away from casework. Booth is helping the FBI as an instructor and Brennan is working with museum artifacts, but Jared’s death pulls them back into danger. A body initially identified as Booth is actually his brother’s, while the missing Booth is found wounded with Jared’s associates. Brennan returns to examine the evidence, and Booth and Aubrey uncover what Jared had been involved in. The couple soon return to their former work.
The team’s investigations continue alongside Booth and Brennan’s adjustment to being back, with Aubrey taking on greater responsibility at the Bureau. A body bomb critically injures Aubrey and Hodgins. Hodgins initially interprets pain and sensation as signs he may recover, but the damage to his spine leaves him unable to feel below the waist. He pushes Angela away as anger and denial take hold; their relationship has to absorb the permanence of the injury as he begins adapting to life in a wheelchair.
Near the end of the season, Brennan’s recurring nightmares seem connected to a killer who stages victims as puppets, including a woman dressed in Brennan’s donated clothes. The team suspects Brennan’s psychiatrist, Dr. Falk, and Booth arrests him, but Brennan is then abducted from the lab. The final scene reveals that Zack Addy has escaped from the psychiatric hospital and taken his former mentor. Whether Zack is the Puppeteer remains uncertain; the season ends before that question is resolved.