Booth and Brennan are called to the scene where a man's body was found gutted, burned, and hung like a scarecrow on the roof of a Federal Building. Evidence left on the body re-opens a 30-year-old case and links back to Brennan's father. Meanwhile, Zack must defend his dissertation to obtain his doctorate, asking help from a colleague.
The episode begins with a man being shot on a bridge, shoved and tied to a pole, covered with gasoline, and burned. The audience is only able to see the silhouette of the man who killed him.
We then cut to Zack Addy, defending his dissertation in front of several other doctors on the Committee (one of whom is his former teacher and current senior, Dr. Temperance Brennan), as the last step towards getting his doctoral degree. Booth arrives to get Brennan to take her the murder scene; while Brennan is upset at having to leave Zack, Booth acts indifferent towards him. After they leave, Professor Constance Wright asks Zack how he expects anyone to take him seriously when he looks the way he does.
At the crime scene, Brennan discovers that the corpse has something jammed down its throat; back at the Jeffersonian, it is shown to be a coin with a picture of Christopher Columbus's face on it and a piece of paper identifying the man as Garrett Delaney, an ex-FBI agent. Brennan's brother Russ visits her, telling her both that their father called warning them of danger and that he (Russ) can sense that he is being watched, leading Temperance to invite him to stay with her for a few days. In Delaney's apartment, Booth and Brennan find a room filled with pictures of Russ, confirming that he was being stalked. Due to the sniper's range in the pictures, they realize that someone was hunting Russ to kill him.
Angela and Hodgins scan the piece of paper, on which an FBI agent named Gus Harper wrote that he would not help to frame a man named Marvin Beckett, a politically powerful African American rights activist whom the FBI was opposed to, and who was later sentenced to life in prison -- for the murder for Gus Harper. They realize that the FBI killed Harper when he refused to help frame Beckett, then framed Beckett for Harper's murder themselves to discredit him. Harper's wife reveals that Harper had been compiling evidence against the people who were trying to frame Beckett, and hid the evidence in a bank's safe deposit box. Realizing that her parents robbed that bank and stole the evidence, Brennan discusses this with Booth and Russ, and they realize that Russ' and Brennan's father, Max Keenan, was code-named Columbus, and killed Delaney to stop him from killing Russ.
When asked, Zack tells Dr. Brennan that he does not feel worried about his doctorate and that some people on the board like him, as one scientist patted him on the shoulder with an open hand -- which, according to a body language book Zack read, is a sign of approval. Though Brennan seems skeptical of this, she pats his shoulder in this way when she walks away, pleasing him.
Booth talks to Caroline Julian in the cafe the next day, and they decide to try to get Marvin Beckett acquitted of his charges. Russ brings a priest, Father Toby Coulter, who claims to be the lifelong best friend of Max, to the Jeffersonian. Father Coulter says he has a message from Max, that he wants his kids to drop the case and that Max loves them. They suspect that, in order to force Max to hand over the evidence he stole from the bank years earlier, Delaney targeted Russ. Booth and Caroline manage to convince the judge to reopen the Beckett case and allow the Jeffersonian to perform an autopsy on Harper to determine whether or not Harper was killed as was claimed. The team manages to prove that not all of the bullets in Harper came from the revolver that was assumed to be the murder weapon; some came from a sniper's rifle. That night, when Booth meets with Russ at the diner to talk about the latter's parole violation, Russ is shot at and almost killed by a sniper.
Due to the inconsistencies in Harper's death, Beckett is released from jail. The triumph of this success is short-lived, though; this event causes FBI Deputy Director Kirby to chew out Booth and "suspend him without pay" (which, according to Cam, is FBI-speak for fired). However, all of Booth's Jeffersonian colleagues want to help him, believing the best way for him to get his job back is to solve the case. They discover that Harper was killed by a military rifle with homemade rounds. Brennan realizes that if she can get her dad to give her the evidence he stole, she'll be able to get Booth's suspension lifted. She later discovers from Father Coulter that Booth has put surveillance on him, and is upset that Booth didn't tell her. They disagree about her father – Brennan is angry that he abandoned her and killed numerous people, and while Booth also disapproves, he holds a certain amount of respect for Max's determination to protect his family at all costs, even if the costs are extreme.
Zack asks Dr. Saroyan if she'll give him a job when he gets his doctorate, but she tells him that an important part of their job is appearing in court, and as he looks now, no one will take him seriously. Zack goes to Angela's office to ask for her help, and, after a bit of persuasion, she agrees.
Though Caroline's own job is in jeopardy, she brings Brennan and Booth the sniper's list they asked for. She also brings Marvin Beckett to the Jeffersonian so that he can both thank Booth and Brennan for gaining his freedom and warn them about the people they are up against. After looking at the list and seeing Deputy Director Kirby's name on it, they realize that he is the sniper who is trying to kill Russ. They call Russ to warn him, but he doesn't answer, so they go to Brennan's apartment only to find nothing but a giant pool of blood on the floor – an amount no one could survive losing. Believing it to be Russ' blood, Brennan is hysterical, but Booth manages to calm her. Cam later uses blood typing to determine that the blood cannot belong to Russ.
While Brennan meets Father Coulter in a park, Booth meets Caroline in the diner. She informs him that the person named Toby Coulter is actually a bedridden, 90-year-man, and thus Booth knows the man Brennan is with is an impostor. He rushes away in Caroline's car, believing Bones to be in danger. During his conversation with Brennan, Father Coulter recalls a past memory of Max and Brennan when she was small, and inadvertently refers to himself in the memory, revealing himself to really be Max. Bones is disappointed that she didn't recognize him sooner based on the tell-tale signs of cosmetic surgery, hair color, and colored contacts.
Max reveals that Russ knew his true identity from the beginning. Brennan seems to be hurt that Max revealed himself to Russ and not to her, but Max replies that she does better without him, while Russ does worse. He explains that he didn't hand over the evidence to the authorities because his wife Christine felt that if they did, the whole family would be killed, and adds that he is constantly heartbroken by the fact that Christine died anyway. He gives Brennan the key to the safe-deposit box where he has hidden the evidence; Russ then drives up in his car to pick up Max. Brennan tries to handcuff Max, but he overpowers her and handcuffs her to a bench instead, then moves to leave with Russ (though not before telling Temperance to hold on to the ones she can trust, that he's proud of her, and that he loves her). Booth arrives, and Max tells him to take care of Temperance. Booth starts to arrest him, but lets him escape at Brennan's unspoken request. He frees her from the fence as Russ backs his SUV into Caroline's car in order to disable it, much to Booth's chagrin, then he and Max drive away. Max is then shown hanging Kirby's body and burning it in the same way he burned Delaney's body at the beginning of the episode.
Zack comes to ask Doctor Saroyan for a job again after being made over by Angela; he now has short hair and is wearing a suit, looking much more businesslike. After Zack promises to learn how to act in court, Cam grants his request for a job. They decide to celebrate at the diner, and Zack gains approval from all of his colleagues; Hodgins slips a hat on his head, Angela kisses him on the cheek, Cam pats his arm, and Brennan gives him a big hug, calling him by his new title, "Dr. Addy."
At the diner, Booth arrives and tells Brennan that, thanks to the evidence that she got from her father, Booth got his job back. He also tells her of Kirby's death, and that it was Kirby's blood in her apartment. He says that Max loves her, and he burned Kirby's body as a warning to others to stay away from her. He is sympathetic that Brennan had to watch her family drive off without her again. Zack sees Booth with Brennan and waves them both inside. Booth is reluctant to join, but Brennan convinces him to do so, and asks him to pat Zack on the shoulder with an open hand.
- Temperance Brennan - Emily Deschanel
- Seeley Booth - David Boreanaz
- Jack Hodgins - T.J Thyne
- Angela Montenegro - Michaela Conlin
- Zack Addy - Eric Millegan
- Camille Saroyan - Tamara Taylor
- Robert Kirby - Ryan Cutrona
- Barbara Harper - Barbara Williams
- Judge Ted Kemper - Madison Mason
- Marvin Beckett - Lou Beatty Jr.
- Asst. U.S. Attorney Dan Burridge - Bryan Cuprill
- Professor Constance Wright - Kathy Reichs
- "Running Up That Hill" - Placebo
- "Sea Lion" - Sage Francis
- This is the first episode when we see how the victim was killed (in this case burned) before the team discovers the remains.
- This episode marks the first appearance of Temperance's father, Max Keenan, although he already appeared during flashbacks in The Woman in Limbo, where he was played by a different actor. Temperance makes a reference to this by noticing Max's dyed hair, contact lenses and facial plastic surgery.
- Although Brennan's father had drastically altered his appearance and aged 15 years since she'd seen him, she still should have been able to identify his voice, especially since she recognized his voice from the message he left on her answering machine in the last episode of season one (presumably only a few months earlier).
- When Brennan is talking to the priest and he tells her that her father came to see him to confess, she states that her family isn't Catholic. But in the Temperance Brennan novel series written by Kathy Reichs, from which her character is based, it is stated that she is Catholic.
- Author Kathy Reichs, whose books the series is based on, appears as one of the panelists quizzing Zack on his dissertation.
- Because of filming curfews in downtown Los Angeles, the opening scene with a burning body had to be filmed in the day rather than a night. A technique called 'day for night' was used to make the change.
- When Booth hands Brennan a list of bank robbers with their code names, a close up shot is seen of a section of the list. The section includes 2 fake names, 2 character names, and four other names.These are Jan Dewitt, producer, Steve Beers, co-executive producer, Maggie Parker, 1st asst director, and Kent Henzlinger, 1st asst director.
- This was Joseph Ruskin's final on screen role before his death on December 28, 2013 at the age of 89.
- After Bones, Booth, Russ, and "Father Coulter" watch the news report about Marvin Beckett in Booth's office, "Father Coulter" pats Russ with an open hand on his shoulder as he says, "To think that some people still refuse to believe in guardian angels." Zack earlier stated this was a gesture of approval between an older man and a younger man - which makes sense later when the priest's identity is revealed.
- The coin that is found is either a 1892 or 1893 Columbian half dollar, the first United States commemorative coin. It was issued both to raise funds for the 1893 World's Columbian Exposition and to mark the quadricentennial of the first voyage to the Americas of Christopher Columbus, whose portrait it bears.
- At the very end of the episode, Deputy director of FBI Kirby getting killed wasn’t investigated enough considering their arguments with Agent Booth and his suspension from FBI. And also Booth went through an assassination attempt by Kirby during contacting with his very killer’s son, Russ Brennan. It appears to be suspicious from an outer view, yet it is not investigated enough in the show.
The Headless Witch in the Woods
The Man in the Cell
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