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Hayes Flynn was a by-the-books FBI agent who worked to bring Christopher Pelant to justice. He worked in Domestic Terrorism but took over Pelant's case when Booth was taken off it. When Booth went back to managing Major Crimes, Flynn was happy to give control back over to him. In The Corpse on the Canopy, Flynn 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 in The Sense in the Sacrifice by Christopher Pelant, he was skinned and burned while performing a task for Temperance Brennan and Lance Sweets with the goal of luring Pelant out of hiding. Seeley Booth did not agree with the task at hand but went along with it to try and catch Pelant. FBI found stacks of cash in his refrigerator, leading some to believe that Flynn was working for Pelant. Agent Booth adamantly denies this and believes wholeheartedly in Flynn's innocence. 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.
- The Next in the Last (Mentioned)