Hayes Flynn was a by-the-books FBI agent who worked to bring Temperance Brennan to justice when Christopher Pelant framed her for the murder of Ethan Sawyer. When Booth was demoted to desk work after assaulting Pelant, Flynn took over the case and the Major Crimes unit. The squints frequently clashed with Flynn while attempting to clear Brennan. After Pelant was captured and Booth reinstated, Flynn moved to working at Domestic Terrorism.
In The Corpse on the Canopy, Flynn took part in the investigation until he was shot multiple times by a machine gun remotely activated by Pelant. He was not killed but it effectively ended his work in the field. He was permantely assigned to desk work which he disliked.
He was killed by Pelant in The Sense in the Sacrifice, while setting up a fake corpse for Brennan and Sweets with the goal of luring Pelant out of hiding. The FBI later found stacks of cash in his refrigerator, leading Sweets to believe that Flynn was working for Pelant, though Booth adamantly denied this and believed wholeheartedly in Flynn's innocence. The squints discovered that there was a tooth in Flynn's stomach. This was purposely done as he had learned that Brennan solved a murder with only a tooth. Flynn swallowed his own tooth so the team could get revenge for his death. Later, Pelant confesses that Flynn had no knowledge of the cash in his refrigerator or that Pelant had planted a bug in his car, thus proving his innocence.