Brennan and Booth arrive at a mansion where they're told a dead body was found. Brennan asks Booth how therapy's going and he'd rather not talk about it. Inside Cam greets them and leads them to the victim that's been decomposing for three weeks. She says that it's probably the owner of the house because the wife ID'd his watching and wedding band. Brennan wonders why she's there if the body still has flesh on it and Cam explains that the dead man, Mr. Terry Bancroft, is responsible for the Bancroft wing of the Jeffersonian. They asked for Brennan and team by name.Booth sits in the kitchen talking with Mrs. Clarrisa Bancroft. She claims that she's been away at their vineyard and that he was supposed to be at their fishing lodge. She tells Booth that she heard it might have been a break in, and she goes on to say that Terry was involved in a youth center for inner city kids and they might want to look for the killer there.
At the lab, Cam, Zack, and Hodgins discuss evidence they've already found. Cam says that Terry was stabbed in the chest after he was dead and that a slash in his jugular killed him. Zack runs the dental records and gets a positive match to Terry Bancroft. Hodgins seems tense.On the forensic platform Hodgins goes through some photos found on the victim's desk as Angela approaches to tell him that she's got more evidence for him in his lab. Angela exits and Hodgins goes back to a photo a four boys which on the back says, "Me, Hodgins, Stoner, and Tripp before our first gig. August '95." Hodgins pockets the photo.
Brennan is joined in her office by Agent Sully, who invites her to come see him play in a basketball game. Brennan doesn't seem interested.
At the Bancroft mansion, Hodgins comes to the door to meet Clarrisa Bancroft. She's surprised to see him because she knows him. In fact, they have a romantic past. Hodgins tells her that they have to pretend not to know each other because if anyone finds out he'll be taken off the case. She agrees to keep the secret.Booth is at The Go To Youth Center talking to the director, Robert Fraiser. Booth asks about any strange recent activity and Fraiser tells him that Terry did find one of the youth center kids with a couple pounds a heroin on him and took it. They check out the locker of the kid who was holding the heroin, Julio, and find a sweatshirt with blood on it.At the lab, Angela and Brennan find a mark on one of the vertebrae. She then asks Angela for advice about going to Sully's basketball game.
At the FBI, Sully asks Booth for advice on Brennan, but Booth doesn't fell comfortable. Booth s then alerted that the city coroner might have found their suspect Julio.At the coroner, they ID the body as Julio and find that he was shot in the back of the head. They'd had his body for a while. They conclude that the drug runners that killed Julio probably killed Terry as well.
At the lab, Zack finds evidence that Terry was killed and laid on his back for hours before he was put in the chair, tied up, and stabbed. Hodgins comes in with evidence from lava found on the body that the body has been dead 18.5 days, which means Terry died after Julio's body was found.
Brennan enjoys Sully's basketball game and finds out that his nickname is "Peanut".Booth meets with Dr. Wyatt at the diner and they discuss his mental wellbeing.
At the lab, Hodgins tells Booth that he found Indian ink from a letter opener in the victim's throat along with a muskrat hair. Booth gets to thinking and asks Hodgins to come to the Bancroft house so he can find out if she was cheating on the husband.
At the Bancroft house, Booth gets Clarissa to spill he guts about her affair while Hodgins looks for evidence in the other room. Booth gets his name, Leland Oliver, and then also finds out about she and Hodgins relationship. Booth tells Hodgins he's in deep trouble.At the lab, they link the muskrat hair to a jacket worn by The Go To director, Robert Fraiser, but then Booth tells them about Hodgins relationship with the victim and they realize that the evidence he's found is now useless. They give Hodgins the third degree and tell him how he's compromised their case, but he just wanted to find his friend's killer.
In court the team tries to prove the case by submitting their evidence to the jury. While Booth is on the stand he's interrupted by Luiz, a kid from The Go To. He says that he saw Terry take the dope from Julio and that he'll testify if it will help. On the stand, Luiz gives them the witness they needed.Just when they gang think things are moving their way, the defense uses Hodgins involvement in the case against them.
With the playing field completely leveled in court, Brennan and they gang have 24 hours to come up with new evidence to convict Fraiser without Hodgins help.At the lab, Brennan finds a fungus on the victim and the inspect it. Hodgins arrives and gives Cam his letter of resignation. No one is happy about this. Back to the fungus, which is Hodgins' specialty, Angela looks over Zack's shoulder and helps him. Apparently she's been spending a lot of time with Hodgins cause she knows a lot!At the diner, Hodgins sits with Booth, who's not too happy with Hodgins. Hodgins tells him that he's resigned and they're square again.
In court they present their fungus evidence and the fact that they found the same fungus on the defendant. They find him guilty and Hodgins gets his job back.