Season synopsis
Contains spoilers for this season and earlier seasons.
Season 12 begins seconds after Zack takes Brennan from the Jeffersonian. She realizes he is not the Puppeteer: Zack was trying to protect her from his psychiatrist, Mihir Roshan, who had committed the murders and framed his patient. Zack is returned to custody, and the team continues investigating the old Gormogon case that put him there. Hodgins also learns that the feeling in his legs does not mean he will walk again; he and Angela face the injury as a lasting change rather than a temporary setback.
Booth’s past as a military sniper resurfaces when Mark Kovac, son of a man Booth killed in Kosovo, targets him and his family. Max is killed while protecting the children, and the team works to stop Kovac’s coordinated attacks. In a separate case, Hodgins finds evidence that helps clear Zack of a murder he did not commit. Zack is exonerated on that charge, though he must serve the remaining sentence for helping Gormogon. Cam and Arastoo marry as the team’s personal futures also come into focus.
Kovac escapes and plants bombs at the Jeffersonian, where Booth, Brennan, Hodgins and Angela are trapped when the forensic lab is wrecked. They survive, but Brennan has a head injury that temporarily prevents her from drawing complex conclusions. With the interns using what she taught them, the team locates Kovac; Brennan’s reasoning returns in the crisis, and Booth kills him. Afterward, Cam takes six months off to welcome three adopted sons with Arastoo and promotes Hodgins to direct the lab. Angela and Hodgins prepare for another child, while Booth and Brennan choose to keep their partnership and return to their lives together.