The milestone 100th episode takes back in time 6 years as Brennan and Booth recount the first case they worked on together. With Sweets finishing his book on their partnership, Brennan and Booth take this opportunity to set the record straight. A young and rebellious FBI Agent Booth seeks the help of an team of anthropological scientists and a street artist to find the evidence that will prove his high-profile suspect guilty. Although in unfamiliar territory, Dr. Brennan, her grad student Zack, Hodgins and street artist Angela get right to work, impressing Booth with their knack for uncovering new leads and substantiating his theory about a well-connected district judge. While the case cements a foundation for a successful future partnership, it also reveals the convoluted romantic beginnings of the formidable duo — whose feelings for each other almost destroyed the team but still linger years later.
Booth and Bones walk to the office carrying manuscripts of Sweets' book. They talk about how Sweets has his facts wrong. Bones explains that the first case the two worked on together is not the one mentioned in the book. Booth is disappointed. He thought the mistake was "the whole 'love thing', but Bones doesn't care about that. Inside, Sweets is aghast. Turns out his entire thesis about the Bones-Booth dynamic was based on that erroneous first case. "Please tell me all about that real first case to see if my conclusions are valid," the psychologist begs.
We open with cocky, gelled-hair-combed-over-and-strictly-parted Booth playing pool for cash and winning. He gets a call from a murdered girl's mother who is upset that the cops are about to close the unsolved case. So Booth heads to meet Camille, then-Chief Coroner of New York with custody of the remains, who suggests he partner with Brennan. He is unenthusiastic, but he agrees to meet Brennan anyway and is surprised to discover she is not only brilliant, but also beautiful. "Do you believe in fate?" he asks. "Absolutely not. Ludicrous." she says.
Cut to Brennan examining the body with Zack. Hodgins approaches and gets very excited to learn his colleagues are working on a body which isn't 200 years old. Later, Brennan visits Angela, working as a street artist. The former asks the latter to draw a caricature based on the victim's skull. Angela immediately agrees after being told she would be paid as she is saving to "go back to Paris."
So Brennan brings Booth a super-detailed sketch along with news the victim was 16 years old, biracial and probably a singer. Booth is awestruck, but Brennan doesn't notice. She does agree to adapt to handling evidence with gloves from then on. "I'm sorry we couldn't find a name," Brennan says. Booth then reveals he knew the identity of the victim all along, he was simply testing the Jeffersonian team. He then says he knows a federal judge is responsible for the death. She asks how and he says that he just knows. Brennan only agrees to find the truth.
Hodgins quickly finds a splinter of wood in the body and the girl's boyfriend was in town to try out for a minor-league baseball team four years ago when she was killed. The team also uses wooden baseball bats. Hodgins doesn't think that a baseball bat is the murder weapon, so Brennan suggests that he and Zack conduct an experiment to determine if this was possible, which neither of them are happy about. Meanwhile, Booth isn't excited about bringing in the boyfriend because, he "knows" that the judge did it. But he wants to convince Brennan, so with Brennan asking to watch Booth "broil" him they question the young man, who protests his innocence and still appears to be grieving.
Later, after doing the experiment in which both he and Brennan whack a well-padded Zack, Hodgins concludes a baseball bat could not be the murder weapon. Cut to Booth and Brennan investigating the performance hall where the victim performed before she went missing. Booth decides to call Brennan "Bones", which prompts her to offer to call him "Shoes", since his are so shiny. Booth, wearing a black tie, black socks, and the aforementioned shiny black shoes, says that they're part of his FBI uniform. Brennan points out that although paramilitaristic organizations tend to constrain individuality, but the "freethinkers, mavericks, rebels" with leadership qualities find ways to declare their distinctiveness. Bones then asks Booth straight out if he is attached, and subsequently indicates she would be interested in dating him, who explains such "fraternizing" is against bureau policy. They then stop at a flight of wooden stairs. It's possible the victim fell down the stairs or was dragged down. An exit to an alley is nearby.
With Angela there to provide a "reconstruction", animated by flipping through a sketchbook of stick figures, Booth presents his case to Caroline, who is skeptical as usual. She doesn't believe the judge dragged the victim to his car in the alley and then drove to the dump site. Caroline then more or less kicks the two out of her office without bothering to remember Brennan's name, because according to her squints tend to get all "wishy-washy and flip-floppy" on the witness stand. So Booth decides to question the judge, inviting him to the performance hall. The judge denies everything and insults Bones, so she punches him in the face. Caroline is not and advises Booth to "cut all ties" with the doctor. Angela, meanwhile, notes the head had a noticeable dent in it perhaps from a car door, while Brennan regrets having Zack boil the flesh off the bones and potentially get rid of particulates that Hodgins might have been able to identify.
Later, Booth and Bones are getting drunk at a bar together. He shows her the cheeky underside of his red tie. "You're fired," Booth says. "You assaulted a federal judge." He explains it was "hot," but he is just following Caroline's orders. "If we don't work together anymore, we can have sex," Bones whispers. The two rush outside into the rain and begin kissing. In present day, Sweets is shocked and questions how long the affair lasted. Back in time, Bones breaks the kiss and declares they're "not spending the night together" because she is drunk. Sweets collapses on his couch in despair.
The next morning, Bones is hung over and informs the excited team they have been fired because of the assaulting-the-judge incident. Angela loses hope of ever going back to Paris, but Brennan offers her a job reconstructing ancient remains and tombs and digs, while Hodgins says he's always wanted to go to Paris with an artist. "Take all of the evidence to Booth at the FBI, and we all go back to our normal jobs," Brennan says. So Zack takes a file folder to Booth and calls the agent "stupid" for firing the team. All the proof to nail the judge is in the folder. Cam takes a look and informs Booth that the victim was killed by the locking mechanism in the judge's distinctive car, and "they got the judge". Caroline tells Booth to hire back the Jeffersonian team.
So the two use their warrant to tear apart the judge's classic vehicle. After Booth's people can't find anything, Bones steps in and immediately discovers a bone fragment. She is also upset at Booth for getting her drunk and tells him as much, though he claims he got himself drunk to fire her. The two bicker as Booth arrests the judge. Later, he admits the victim caught him snorting drugs and he only tried to catch her when she ran. She fell down the stairs and lost consciousness, but he thought that he killed her, so he brought his car around and was putting her in the trunk when she woke up. He panicked and slammed the lid down on her head, which is when he actually killed her.
Cut to the present. "It's like you two missed your moment and you ended up punishing each other for it," Sweets observes, lamenting that he is the one who ends up paying the price. In fact, the two explain how they began to argue soon after the judge's confession, unknowingly hitting all of each other's sensitivities, causing Bones to slap Booth across the face. She then swore never to work with him again, calling him a "bully." She says that it took another year before they were able to be in the same room with each other. Sweets urges Booth to break the stalemate, be a gambler and declare his love for Bones. The two smirk and leave.
Outside, Booth stops and faces Bones. "I'm the gambler," Booth says. "I want to give this a shot." He then leans in and KISSES Bones. He confesses that he always knew that she was the one for him, but Bones backs away terrified and begins to cry. She rejects him and wonders if they can still be together. Booth says they can still work together, but he "has to move on" when it comes to romance. "I know," Bones says. They walk together into the night.
- Temperance Brennan - Emily Deschanel
- Seeley Booth - David Boreanaz
- Jack Hodgins - T.J Thyne
- Angela Montenegro - Michaela Conlin
- Camille Saroyan - Tamara Taylor
- Lance Sweets - John Francis Daley
- Zack Addy - Eric Millegan
- Caroline Julian - Patricia Belcher
- Judge Myles Hasty - Seth Isler
- Tucker Henry - Theodore Borders
- Jocelyn Arrington - Angela Elayne Gibbs
- Gemma Arrington - Laura Izibor
- "Mmm" - Laura Izibor
- "One Beats Three" - Bear Lake
- Booth is again mentioned to be a descendant of John Wilkes Booth, as Brennan said, by his bone structure.
- Booth defines to Zack while in his office why he refers to scientists as "squints". "You know, when you look at things, you squint. Like that."
- Cam and Brennan meet in this episode, which happened before the first season, because this is Brennan's and Booth's first case together and Cam even mentions meeting Brennan at "a conference on decapitation" despite that Brennan and Cam had claimed not meeting until The Titan on the Tracks, which happens in the second season. However, in that episode, it was shown that Brennan had forgotten that she had met a firefighter working on the train accident scene three times previously, so it is possible that in both episodes she also forgot that she had met Cam previously, and Cam just went along with it when they met for the third time and started working together.
- Also Caroline Julian meets Brennan for the first time. Despite in season 1 episode The Man in the Morgue, when Booth brings in Miss Julian to help Brennan, that Brennan and Caroline had meeting and being introduced eachother by Booth, it's clear that this is supposed to be their first meeting.
- Sweets says that he thought if Booth and Bones kissed each other, they would finally see they belong together. He acts like it had never happened before this episode except for their first case together. But, in a previous episode, they kissed under the mistletoe.
- There is a quote seen in the final scene, just before Booth confesses his feelings to Brennan: "Nothing happens unless first a dream..." -Carl Sandburg". This is a reference to Booth's coma dream in S4 E26, when he dreams about him and Brennan being married and her becoming pregnant. When he woke up from the dream, Booth realizes how much he loves Brennan.
- Booth mentions an event for a bunch of "hoity-toits"-- which he defines as shakers, makers and intellectual types of people such as Judge Hasty.
- Angela, when she sees Zack for the first time, refers to him as "Jimmy Neutron". Neither he nor Brennan knows what she was talking about.
- Booth(to Bones): I have been wanting to do that for years. You are so hot!
- Hodgins(to Angela, after Brennan tells them they're all fired): Ever feel like you saw something great that almost happened, but then it didn't?
- Booth: Okay, excuse me, you know what, you really need to learn how to speak to human beings.
Brennan: I speak six languages, two of which you've never heard of.
Booth: You know what? You're a cold fish.
Brennan: "You're a superstitious moron.
Booth: Get a soul.
Brennan: Get a brain.
FBI Tech: Agent Booth.
Brennan and Booth: What?
Booth: I'm Agent Booth.
- Booth: I'd ask you out if I could.
Brennan: Why can't you?
Booth: Well FBI rules again. No fraternizing with other agents, or consultants.
Brennan: That's too bad.
Booth: Glad you think so.
The Bones on the Blue Line
The Death of the Queen Bee
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