The "Bones" episode "The Patriot in Purgatory" opens with two pretty amazing sights. The first: a corpse with a chainsaw sticking out of its chest. The second: all of the interns in one room at the same time.
But Bones didn't gathered her top five interns to gawk at the chainsaw corpse (a juggler who drunkenly took on too much): She wants them to identify over 1,000 sets of remains the Jeffersonian hasn't been able to catalogue. Bones is on a major teamwork kick after reading a book on basketball, and she encourages her team of interns to work together (and gives each one a firm pat on the backside).
Each intern identifies a ton of remains, except for Arastoo. The body he is working on was that of a homeless man. Moved by the photo of the body from the police report, he feels compelled to give this man back his identity, no matter how long it takes.
The clues are scant: There are traces of jet fuel in the victim's teeth, as well as a bullet wound from 20 years ago and a bit of shrapnel that was embedded in the rib 10 days before death. The team believes that this homeless man was injured during 9-11 and died after being beaten to death 10 days later.
Booth believes that the homeless victim may have been a Gulf War vet, but the Pentagon says all of their people have been accounted for. He does some further digging and finds that the homeless man was, in fact, a Desert Storm vet named Tim Murphy. That explains the traces of uranium in the remains: He was in a munitions dump that got hit, which released depleted uranium into the environment. Booth and Bones interview Tim's tearful widow, who wishes she could have done more to help her husband.
Back in the lab, Hodgins develops a theory that may help the team discover where Tim was standing when the attack happened. The shrapnel in Tim's ribcage didn't come from the plane, but rather from a group of lamp posts on the west side of the Pentagon that were sheared off during the attack.
Back in Booth's office, Bones and Booth get a visit from one of Booth's contacts in the Pentagon. Apparently, Tim stood outside of the Pentagon every day for a year before his death, yelling at people to "walk in Moore Park." However, there was no Moore Park nearby, and so nobody knew what he was talking about. Booth goes through Tim's belongings and realizes that Tim was actually yelling the names of his army buddies: Walken, Moore, and Park. Tim wrote to the Pentagon 56 times to ask for the Silver Star to be awarded to his three friends, who all died overseas in the munitions dump.
Blood on Murphy's shirt was revealed to have come from three people who worked at the Pentagon that day and survived. Booth and Bones learn that Tim saved those three people who had been trapped under concrete beams. Tim wasn't murdered: The injuries sustained when helping people escape from the Pentagon killed him slowly over 10 days.