Kirby was the ATF Rep on the corrupt FBI Task Force who conspired to plant stolen money on Marvin Beckett. Gus Harper, decided to reveal their plan to the FBI, but Kirby killed him and framed his murder on Marvin Beckett. Years later, he rose through the ranks and became the Deputy Director of the FBI.
Robert Kirby suspended Special Agent Seeley Booth for bringing up the issue of Marvin Beckett being released after being falsely arrested for the murder of FBI Agent Augustus Harper. Kirby also tried to kill Russ and Seeley in the Royal Diner as a warning to the people investigating Harper's death. He recruited Garrett Delaney to take pictures of Russ who he intended to kill to lure Max out of hiding.
Later, Booth and Temperance Brennan find a pool of blood at her house which is found to belong to him. Max Keenan stabbed him with a Misericorde, gutted him, and set him on fire postmortem on a rooftop in the same manner as Garrett Delaney. Max is later arrested for Kirby's murder, however he is acquitted due to his lawyer, David Barron, making it sound like Temperance also had a motive, means, and opportunity to kill Kirby, resulting in Max's release.