In last night's episode, it emerged that Booth's acquaintance Jacob Ripkin Broadsky (Arnold Vosloo) was the person who shot the Gravedigger.
Speaking to TV Line, Boreanaz suggested that Booth previously looked up to Broadsky.
"[Broadsky is] someone who Booth is proud of, somebody that he has respected and learned from in the past," he said. "He knows he's a good guy, but he's kind of gone the wrong way."
Boreanaz continued: "Booth is just looking to answer two questions - Why? And how could somebody do this? Now he might have to take him out - with his own gun - and that should be interesting to see."
Bones airs on Thursdays at 9/8c on Fox.