JFK was first mentioned in The Proof in the Pudding. His body was brought in by Mr. White from the General Services Administration to determine cause of death. Everyone from the Jeffersonian Forensic Team was confined to the facility until they find cause of death. They timed their arrival to make certain that Bones and everyone else would be the only ones in The Jeffersonian. They presented the team with his skeleton and samples which were preserved in a metal suitcase and left for Dr. Hodgins. Mr. White forbade any kind of destructive testing on even the smallest sample or the samples they provided for Hodgins and identification has been regarded as priority zero. Mr. White has his men watch over the team and he even traced all their calls when they were trying to be inconspicuous. They even apprehended Booth in the parking garage after Sweets warned him about what was happening at the Jeffersonian.
Hodgins and Bones were able to determine his identity by observing the Chanel samples from the suitcase and comparing one of the bones with other older bones from Limbo to determine that he died within months of the Limited Test Ban Treaty in 1963. Booth was later able to break into the Jeffersonian, but he was jumped by two of Mr. White's guys. After Bones told him that it was JFK that they are investigating and that Hodgins was the first to determine that it was JFK, Booth concretely refused to believe that it was JFK. Booth determined that the people who apprehended him are with the Secret Service based on the maneuver that they used to pin him to the ground and reported it to Assistant Director Andrew Hacker who was planning to use his contacts in the White House to determine what was happening, despite the fact that Mr. White was listening in on their conversation.
Many of the skull fragments were missing from the skull. Booth thought that they were held back on purpose, but Bones claimed that since Forensic Techniques were relatively primitive in the 1960s, they were never recovered after they were scattered and pulverized as a result of the bullet impact. After Angela did a facial reconstruction, Booth still refused to believe that it was JFK. Mr. White came in and reminded them that they were not permitted to identify the remains, but Bones tried to convince him that they need to encase the skull in flesh to discover cause of death.
The official record based on an animation by the Justice Department was that JFK was shot in the head by Lee Harvey Oswald with a World War ll era Italian Rifle; a 6.5mm Carcano Carbine. JFK's head went back and to the left when he was shot 1.6 seconds before John Connolly who was in front of him at the time. The diameter of the entry wound was the same caliber as the rifle. The president's limo, during the motorcade, was traveling at least 4.5 meters per second; between ten and eleven miles per hour. The team decided to re-enact the assassination with a perfect replica of Lee Harvey Oswald's rifle which was at the storage room at the Jeffersonian in Crate: 01033. Booth and Sweets were able to sneak into the storage room through a ladder hidden behind a false wall in the janitor's closet which Hodgins discovered after checking the claims of a conspiracy group who claimed that the Jeffersonian was a Masonic construction.
The results from the re-enactment were radically different from the official story. Both the targets were shot 1.6 seconds from each other exactly, however there was no wind resistance, no distractions, and Oswald was a lousy shot compared to Booth who was determined by Hodgins to have barely made the shot. Booth still refused to believe that the official story was falsified after running the simulation. Bones discovered that the exit wound on the skull was just another entry wound, which indicates that there was a second gunman, which infuriates Booth who still said that the bones are not JFK despite everything that proved that it truly was JFK. Booth received a call back from Hacker who told him about a congressional committee who wanted to exhume JFK to see if modern forensic methods could tell them anything about the circumstances of his death. Booth confirmed to Hacker that he and everyone else was confined by persons unknown against their will.
Bones re-examined the skeleton and wanted to discover the whole truth about the skeleton, but Mr. White decided to end the investigation after the team only discovered the half-truth about the bones. Booth decided to help Bones tie up the loose ends by apprehending Mr. White and the other three Secret Service agents while Bones tests both of JFK's radii. Hacker came in later with a S.W.A.T. team right after Booth took them down. Bones tested the radii with two tubs of chocolate pudding with a thickening agent to adjust the specific gravity. One of the radii sank and the other one floated. The radius that was floating was riddled with osteomyelitis, and Bones told Booth that JFK never had osteomyelitis, which makes him proud of Bones for uncovering the truth; his truth. Hacker told Booth and Bones, after talking to Mr. White, that any reports they write on the subject should be carefully worded. (A.K.A. having no words at all.)
Afterwards in The Royal Diner, everyone expressed their thoughts that they were all being tested. Booth because of his post-surgery condition in regards to his brain tumor, Hodgins because of his role as a "paranoid conspiracy theorist," and Cam to see if she could run the lab in a professional manner. Angela thought that everyone failed, but Brennan said that she succeeded in their test because she uncovered the truth. Hodgins told them that there was a congressional committee trying to exhume JFK and discovered that the team was a dry run, hence the demand they were given to not mark the bones. Cam told Bones that JFK had Scarlet Fever in his childhood, which can cause osteomyelitis, but Brennan told her that it was a one in a hundred probability and that it was statistically unlikely that it was JFK because of it. Cam discovered that Bones knew that the remains were JFK, but she lied to Booth to spare his feelings. As Booth and Brennan were leaving the Royal Diner and talking to each other about the case, the Channel 8 news revealed that the congressional committee was denied the motion to exhume JFK citing "respect for the family."
He was mentioned again in The Lance to the Heart. JFK was recorded by a wire recorder during a meeting about the Cuban Missile Crisis sometime between October 16-28, 1962. He was believed to be having an affair with a woman he worked with named "Alice." It's existence implies that he was also blackmailed by the conspiracy used by Desmond Wilson when he had received J. Edgar Hoover's blackmail files before he passed them on to his stepson; Glen Durant. He may have also been assassinated because he very likely refused to be blackmailed by Wilson any longer.
Wire Recorder Playback Edit
- JFK: I will not just ignore the introduction of offensive weapons into Cuba! Make that very clear in the statement.
- Unknown Representative: Yes, Mr. President.
- JFK: That's all for now.... Alice. Stay back a moment, please.
- Alice: Of course, Mr. President.
- JFK: You're looking very lovely this evening.
- Alice: Thank you, Mr. President.
- JFK: I've been waiting for this moment all day. Why don't I take off my--
(Recording stopped by Bones.)
- JFK was buried at Arlington National Cemetery in a mahogany coffin, but Bones determined that skeletonization could have occurred if the casket was compromised.
- After he was shot, the funeral home tried a cosmetic fix with wig hair, wax, and a metal mesh holding it in place which caused a criss-cross pattern on the skull.
- According to Hodgins, JFK was on steroids to treat Addison's Disease and it caused damage to his back and adrenals.
- Cam noted that Kennedy had Scarlet Fever in his childhood which can cause Osteomyelitis.
- In the facial reconstruction, Sweets claimed to see Ricky Martin, Hodgins saw Alex Trebek, Cam saw James Garner, and Bones even thought that the image looked like Booth, which scares him.
- The events in The Proof in the Pudding were most definitely a precursor to the events involving Glen Durant's Shadow Government as the team discovered a trace of the blackmail files in the form of a wire used in a wire recorder which recorded a conversation that implied that JFK was having an affair with a woman named "Alice".