Booth and Brennan make their way through a decrepit bus yard to a skeleton that has been discovered, positioned in a circle. Booth mentions a possibility: the victim was rolled up in a carpet and the carpet has since rotted away. Brennan cracks up, knowing that would have taken thousands of years. Caroline Julian arrives on scene and is taken aback by this side of Brennan; who knew she could laugh? According to Caroline, Brennan is suspended from all crime-related duties while her father's murder trial goes on. She shouldn't be working with Booth, the arresting officer, during that time. Caroline leaves and the partners look to the interesting case Brennan will be missing out on. Brennan knows Booth can't solve the case without her.
At the diner, Booth and Brennan inform Dr. Sweets of the situation. Sweets believes he should have been informed of the upcoming murder trial, seeing as he did the psych profile on Max Keenan, Brennan's father. He notes the stress Brennan must be feeling as everybody she works with is going to be trying to imprison her father. Brennan assures Sweets it doesn't bother her. But he knows the more objective she appears on the outside, the more troubled she must be on the inside.
In the visiting room of the Federal Detention Facility, Brennan, her brother Russ, her father Max, and his lawyer David Barron meet with Clark Edison, who will be the forensic expert on the case. Max isn't fully confident in Clark defending him and wonders why Zack couldn't do it. Brennan tells him Zack will be working for the prosecution but assures her father, Clark is the last forensic Anthropologist she'd ever want to go up against in court. With a hearty handshake, Max reluctantly welcomes Clark to the team. Clark, Russ and Dave leave and Brennan gives Max a gray tie to wear in court. She tells her father that even though her friends are involved in the case, she can't help him. Max knows that, and he also knows his daughter loves him.
In the lab, the squints watch from the sidelines as Brennan, Clark and David look over the bones of Deputy Director Kirby, the victim in Max's case. Angela doesn't like how the team is split up, with Brennan on the other side. Cam assures her, it's a court case, not a competition. Angela can accept that as long as they walk out of the unfortunate situation with their friendships still intact.
Zack, Hodgins, Angela and Cam leave the other team to work with the bones. Clark wants to run his own examination on the body. David notes that the victim was stabbed, set on fire and gutted. It was a merciless death. But Clark sees it differently. Kirby was killed with a single blow to the head. The stabbing, the gutting, the fire, it all occurred post mortem. The team debates the differences between how Clark and Zack will appear on the stand. Brennan thinks Zack will be more precise, but David seems to think Clark will be more understandable and persuasive to the jury. David is going to make Zack look bad and he doesn't want the jury to see Brennan doubting him. It doesn't matter whether they believe Max is or isn't guilty, it's the prosecution's job to prove he is guilty. Seeing as Brennan taught Zack, Clark would like to get a look at some past case files; he wants to know what he's going to be up against.
In the FBI conference room, Caroline speaks with the prosecuting team: Booth, Cam, Hodgins, Zack, Angela and Sweets. She wants the group to know that this trial is going to be no different than any other trial. They aren't buying it though. And to ensure a victory, Caroline runs down the line of what each member of the team will and will not being doing during the trial: Booth won't be wearing his "cocky" belt buckle, no "resist authority" buttons from Hodgins, no self-administered hair-cuts the day before the trial for Zack.
Caroline informs Angela to "ugly it up" so the plain woman on the jury don't hate her. Caroline wants Cam to eat something before taking the stand, to keep her roaring stomach quiet. And it would help the team if Sweets were to use grown up words while testifying. After Angela decides she isn't going to testify, Booth assures the team that Brennan would want them to go through with it. Brennan believes in the system, he reminds them.
In the court room, the no nonsense Judge Marcus Haddoes kicks off the trial. Caroline and David go back and forth pleading their cases. While Caroline paints Max as a cold-blooded killer, David shows Max as a man with many enemies, enemies who wanted him dead. Max was acting in self-defense.
Out in the court corridor, Booth and Brennan talk over coffee. As they aren't allowed to be discussing the case, they cover their mouths with the cups while whispering about Angela's lack of involvement. Booth tells Brennan how Angela refused to testify and Brennan doesn't understand. Zack is the only one who doesn't seem to have a problem testifying against Max and Brennan states that Zack is the only one thinking clearly. Booth has to get back inside because he's the first prosecution witness up.
On the stand, Booth explains how he and Brennan entered the apartment to find a large pool of blood. Caroline asks who they believed the blood to belong to. Cam, next on the stand, shows the DNA analysis to the jury. It proves the blood belonged to Deputy Director Kirby. Cam shows a graphic of where, on the skull, the murder weapon entered, before it cut the victim's carotid artery. Zack shows the path the weapon took to reach the artery. Cam notes that in order for the pool of blood to expand in the way it did, the body would have had to been lying in the same position from three to five minutes. Booth tells Caroline that's about the same amount of time it would have taken to roll the body up in a shower curtain.
Hodgins shows a microscopic image; a piece of copper found in the victim's skull. He tells Caroline the murder weapon was a copper pipe. When asked if he had evidence tying Max to the murder scene, Hodgins points to some dirt particulates he found at the scene, on the rooftop where the body was burned, and the Our Lady of Angels Seminary.
Booth tells the court how he saw the defendant at the seminary the day of the murder. Max was impersonating a priest. Zack is next on the stand. Caroline holds the copper pipe and asks if Zack can tell her, beyond a reasonable doubt, that it is the murder weapon. He can. When asked if there's evidence tying the pipe to the defendant, Booth tells the court when Max was in prison years ago, he used a copper pipe to defend himself against other prisoners. The weapon became Max Keenan's trademark.
A picture taken from the crime scene reveals a pile of ash on a rooftop. The weapon was found amongst the ashes which, Cam points out, were the incinerated intestines of the Deputy Director Kirby. And when Caroline asks how the remains were indentified as Kirby, Angela, on stand, refuses to answer. She swore to tell the truth and the truth is she isn't saying anything. The Judge finds Angela in contempt and he wants her placed in a holding cell until she answers the question. Angela is hauled away in cuffs, but she knows she's right; it's everybody else who is confused.
In the visiting room of the detention facility, Max, Brennan, Russ and David go over the case. The prosecution is successfully painting Max as a horrific man. David mentions bringing Max onto the stand. But how is the jury going to believe Max didn't kill Kirby when his own family doesn't believe him? David considers bringing Russ up to testify but isn't sure if Russ is telling the truth about claiming he didn't witness the murder. He can't put Russ up there if he knows Russ is going to perjure himself. Brennan knows her brother is not lying; Russ did not witness the crime. David leaves and Max tells his children that his conscious is clear. Brennan mentions a clear conscious doesn't point to innocence.
In a holding cell, Brennan tries to convince Angela to testify. But Angela is not going to help sentence her best friend's father to death. This rattles Brennan as she may have overlooked the possibility of the prosecution gunning for the death penalty. Angela thinks Max is going to lose his case and she's not going to be a part of it.
The next day, in the courtroom, Sweets is on the stand citing his credentials. It's an impressive list, including multiple scholarships and Doctorate degrees. The group seems impressed. After Booth and Brennan are caught whispering back and forth, the Judge orders them to be separated. Sweets has compiled a profile of Max over the past six months and is able to tell Caroline that Max is capable of committing murder. He's labeled Max as a man who adheres to his own ethical code. If he feels his family is threatened, Max is a dangerous man, according to Sweets. Caroline shows Sweets a picture of the incinerated victim hanging on a makeshift cross and asks if Max would have been capable of doing such a thing. Sweets feels he could have.
While on the stand being interrogated by Caroline, Russ claims he was not afraid of Deputy Director Kirby, the sniper-trained, corrupt FBI agent who was after him. He knows Kirby was chasing him because Kirby had shot at Russ and wounded him. Russ tells Caroline he was staying at his sister's apartment at the time. Brennan's apartment is where the murder took place. Caroline wonders why, if someone was after him, Russ would leave the safety of his sister's apartment? Russ claims he was on a job interview the day the murder took place. Caroline finds that odd. She wants to know where Russ heard of the job opening.
The court is confused about where Caroline is headed with her line of questioning. When Russ tells Caroline that his father, Max, set up the interview for him, it becomes clear: Max wanted Russ out of the apartment because he knew something was going to happen. Russ assures David that in no way did Max seem as if he was trying to get him out of the apartment the day Kirby was murdered. After David Barron's request for a summary judgment is denied, he tells the judge that the defense will be ready to defend Max that afternoon.
In the lab, Clark goes through Brennan's files. He sprays something on the victim's skull, at the weapons point of entry. From the catwalk, Zack notices this. He wants to know if Clarks found anything on the victim, anything Zack may have missed. Clark doesn't tell him anything.
Outside the courthouse, Brennan catches up with Booth on a bench. Sweets approaches with the news of a book he's writing: a study on efficacy in focused outcomes. He's intrigued as to how Brennan and Booth work so well together and he wants to study them. The partners make a deal with Sweets. They'll allow him to study them for his book and in return he will give them psychological profiling on demand. Booth and Brennan's joking drives Sweets away. Clark approaches with a disk. He's found something...
Back in the courtroom, Brennan, David and Clark huddle together, ready to represent their side. David calls Zack to the stand, where Clark will be questioning him. Clark asks Zack about the murder weapon and Zack, once again, points to the sharp-tipped copper pipe. When Clark brings up a microscopic image of the skull, Zack notices something he missed in his initial evaluation. Microfractures in the skull mean that the weapon went in so deep the hilt hit the bone, causing tiny fractures. Zack's reported murder weapon doesn't have a hilt on it. Clark's successfully proved the prosecution doesn't have a murder weapon. Caroline would like some time to review Clark's findings, meaning that the case is suspended until Booth can find the real murder weapon.
Brennan opens her apartment door to find Booth and Zack. Booth's got a warrant to search the place with Zack as his new "bone guy." While Zack searches the apartment, Booth and Brennan discuss the case. Brennan is confused. She knows her father killed Kirby but she likes the idea of him beating the charge. Booth tells her it's okay if she wants her father to come home, that's normal. But Brennan knows it's her job to put killers away. Booth just wants her to stop thinking with her brain and start thinking with her heart for a change. The moment is broken when Zack finds the murder weapon. Among Brennan's artifacts is a misericorde, a medieval copper dagger.
The court case continues with the new weapon. The squints use the weapon in their explanations and it looks damaging to the defensive. The Judge dismisses court for the day, with David set to remount his defensive the following morning.
The all-but-defeated defense team sits around a table full of take-out Chinese. David tells the group that the case is no longer about forensics. It's now about story and they'll need to show the jury what really happened. Russ thinks his dad should have just run, taken off. But Brennan tells her brother that Max stuck around for her; if he'd left, he'd never see his daughter again. Max can't deny it. Brennan says she's got an idea. She needs to talk to somebody and she leaves the visiting room.
At the diner, Brennan eats breakfast with Booth, where the two, illegally, discuss the case. She's got a way to "lodge reasonable doubt in the jury." And she's going to need Booth's help. Booth agrees, as long as he isn't required to lie on the stand. Brennan isn't sure if she should try and take advantage of the human element of the case. Booth reminds her, "brain and heart."
In the courtroom, Hodgins is on stand. David wants to know if anybody else was at the three locations where the dirt particulates were found. Booth, now on the stand, answers; he was in all three locations as well as Max. David points out that Brennan, too, was at the three locations. David holds up the murder weapon and Brennan admits that it belongs to her. Sweets testifies that Brennan is a totally rational being, enough so to actually rationalize murder. On stand, Booth admits that Brennan had a motive since Kirby attempted to kill her brother. But she was with Booth all day, she wouldn't have had time. David points out that Booth picked his son up from school that day. It would have left Brennan 45 minutes to kill Kirby, plenty of time. Booth, reluctantly, tells the court that even though Brennan could have never committed the murder, she would have had the time to do so.
As the jury returns with their verdict, Brennan stands outside alone. Booth finds her and gives her a hug. Angela comes out and joins them. Caroline and Sweets file out, followed by Max. The free man comes over and gives his daughter a giant hug.