Special Agent Seeley Booth brings Dr. Temperance Brennan and her assistant Zack Addy to an exclusive preparatory school, where a body has been found hanging from a tree. They retrieve the body and return to their lab at the Jeffersonian Institution in Washington, D.C., where they confirm that the body belongs to a teenage boy. Dr. Jack Hodgins determines that the boy died 10 to 14 days earlier.
As Booth asks for a list of students from the headmaster of the school, Brennan calls to tell him of the cochlear implant she found in the victim's ear. She informs him that they will be able to identify the victim by tracing the serial number on the device. The victim is a student of the school, whose name is Nestor Olivos, and is the only son of the Venezuelan ambassador. The team finds it odd that Nestor's hyoid bone is broken, as the hyoid of an adolescent should be flexible and almost unbreakable.
While the school's headmaster and its head of security are adamant that Nestor had committed suicide, Nestor's mother, the Venezuelan ambassador, urges Dr. Brennan to find the truth and believes that Nestor had been murdered. The central mystery of the case is whether Nestor killed himself or was murdered.
Based on the Tabinid maggots's pupal casing, Hodgins determines that Nestor ingested a heavy dose of ketamine, a dissociative anesthetic, before he died. However, the team cannot be certain if the boy had taken the drug involuntarily but Dr. Brennan is able to give a scenario of Nestor's death involving the ketamine. Combined with the ketamine, the choking would have caused Nestor to regurgitate stomach acids, which would have been trapped in the throat and weakened the hyoid bone. The weight of Nestor's body could then be able to break his hyoid.
In addition to the forensic evidence, Dr. Brennan and Agent Booth find DVD recordings of sexual activities, which they discover had led to blackmail. Nestor's classmates Tucker Pattison and Camden Destry had set up a video camera facing Nestor's bed. After Tucker used a video recording to blackmail Camden's mother, he and Camden decided to blackmail Nestor as well. However, when Nestor decided to inform the headmaster of Tucker and Camden's blackmail attempt, they drugged Nestor and hung him on a tree. Dr. Brennan and Agent Booth are able to prove that Nestor was murdered.
Booth is very satisfied, as both the headmaster and head of security will lose their jobs, the sheriff will resign, and both kids are in custody.
After the case, Brennan arrives at a bar where Booth is and gives him his very own ID card which he'll be able to use for future visits.
- Main article: A Boy in the Tree/Characters
- Temperance Brennan - Emily Deschanel
- Seeley Booth - David Boreanaz
- Jack Hodgins - T.J Thyne
- Angela Montenegro - Michaela Conlin
- Zack Addy - Eric Millegan
- Daniel Goodman - Jonathan Adams
- Mickey Santana - Jose Zuniga
- Sid Shapiro - Heavy D
- Naomi in Paleontology
- Tucker Pattison - Toby Hemingway
- Camden Destry - Kayla Mae Maloney
- Melodee Destry - Avis Wrentmore
- Ambassador Olivos - Marlene Forte
- Peter Ronson - Tom Dugan
- Karen Roach - Patrice Quinn
- Leo Sanders - Mark Totty
- Dawn St. James - Mandy June Turpin
- Mr. Destry - Nicholas Hormann
- Tomar Comara - Christopher DerGregorian
- Oraldo - Gary Carlos Cervantes
- Mr. Pattison - Tom Schmid
- Mrs. Pattison - Kristin Carey
- Dr. Theresa Petty - Kavita Patil
- Nestor Olivos - Samuel Carman
- Miles From Monterey (Bernie Remix) by West Indian Girl (Booth and Brennan drive over to inform Nestor Olivos's parents of his death.)
- The City Streets by Positive Flow Feat. Donna Gardier (The gang meets Brennan and Booth at Sid's restaurant.)
- Sunshine Everywhere by Deep Audio (Sid brings over the food and complains about the group's forensic discussion.)
- Cold Hands (Warm Heart) by Brendan Benson (Angela gives Zack advice about women; Booth lays down rules about the ganging hanging out at Sid's; Brennan gives Booth an ID badge for the Jeffersonian.)
- It's revealed that for all Jeffersonian employees to get into the Forensics Area, they must use an ID card to do so.
- Booth eventually gets his own ID card thanks to Brennan.
- Zack: "She said 'Take a hint.' But when I asked 'What hint?', Naomi said if she told me what hint, that it wouldn't be a hint anymore, it would be a statement."
- Zack: "I had sex with Naomi in Paleontology."
Angela: "You mean, actually in Paleontology?"
Zack: "No, at her place. I thought it went great, but I could be wrong, because apparently what I think is wild and kinky is basic. And since she never called me back, I'm wondering if it's because I lack imagination in the sack."
Angela: "You know what, Zack? I'm thinking this is more of a guy-guy conversation."
- The scene right after introducing themselves to security at the school, and being informed they were to be escorted, because they were outsiders...
Booth: Omnia Mea Mecum Porto.
What's that mean, huh?
Regular people stay out?
Brennan and Zack: I carry with me all my things.
- A Boy in the Tree summary at the official site of Bones
- "Bones" A Boy in the Tree (2005) at IMDb.com
- Bones: A Boy in the Tree at TV.com
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