Booth sees that Greg's office looks bare. Booth is told all of the files and equipment of dead agents are removed. Wendy, the agent that shows Booth around, tells him that Greg was a great analyst that found leads the other agents didn't. She explains that Greg pushed the other agents to follow his leads. Wendy says Greg worked late at night on his last assignment. She says she was going to have lunch with Greg over the weekend, but he didn't show up. Booth learns that Greg hesitantly testified against a suspected terrorist named Pedro Marquez. Pedro was detained for over a year until all charges were cleared and he was released last week. Wendy says she thinks Pedro wanted revenge against Greg.

Pedro is brought to the interrogation room. He says after he was released, the government gave him a $100,000 check several days ago for wrongful imprisonment. Pedro he says he was working last Friday at his auto repair shop. Bones and Booth tell Pedro they think he tortured Greg using equipment from his work. Pedro asks them to testify against him in court so he can collect more money.

Later, Wendall tells Bones that Greg fractured his ankle twice during an obstacle course while trying to apply to be a CIA field agent. Bones says it doesn't make sense that Greg went on a physically challenging mission. Wendall says Greg probably saw an opportunity to live out his dream to be a superspy. Wendall admits it was his dream to work with Bones. Wendall says the cavity in Greg's body appears to be too smooth to be made by a drill bit. Bones tells Wendall he did excellent work and that it will be sad to see him go. Wendall is surprised to learn that his scholarship and internship lost its funding. Wendall asks if she can hold a place for him and she says she can't. Hodgins informs Bones that he found a surveillance bug on Greg. Wendall tells Hodgins he just found out he lost his scholarship.

Bones sees that Booth hurt himself while trying to fix his own plumbing. They call in Wendy after they learn she checked out the bug found on Greg. Wendy says she wanted to make sure Greg was not cheating on her. Wendy says they are not supposed to date and implies Booth and Bones are sleeping with each other. Wendy says Greg broke up with her by sending him a photo of himself waving goodbye. Wendy says she overheard Rutledge and Greg argue about diamonds. Angela and Hodgins examine the photo and find a hidden code.

Bones brings Booth a Plumbing for Dummies book that he was looking for. Bones says he can pay him back later. Booth says he is willing to show her how to fix his plumbing.

Wendall finds a wound on Greg caused by a precise attack taught to CIA field agents. They suspect that Rutledge is Greg's killer. Bones and Booth are informed by Harold that Rutledge worked in Russia and Afghanistan where he specialized in interrogation techniques. They figure that Rutledge might be a double agent. Booth learns that Rutledge ordered the replacement of the security officer with his own agent to allow Antanov to slip in the country without the government knowing. He says the diamonds were going to be used as exchange for political prisoners in Pakistan. Greg found out what he was doing and told him to back off. Booth says that there might have been something other than diamonds in the briefcase.

Cam tells Angela that the CIA is going to arrive to take all of their evidence. Booth asks Wendall to hurry up before the CIA gets there. Wendall says he thinks Greg was bound by his feet and arms and suspended mid-air. He says diamond cutting lasers might have been used to kill Greg. They figure Lena from the diamond company murdered Greg. Rutledge arrives and orders his team to take all of the evidence. Booth shares his findings with Rutledge.

They bring in Lena and ask her what was in the case. Lena says she doesn't know where the case is since Greg didn't talk when she tortured him. Angela calls Booth and tells him she decoded Greg's picture and found a map. The team goes to the location, opens a locker and finds a briefcase. They open the briefcase and find a USB flash drive.

After the case is over, Wendall says goodbye to the team. Cam tells Wendall that he doesn't have to leave because his sponsors received an anonymous donation. Wendall thanks his anonymous donor. Cam says the sponsor received enough money to fund three interns.

Later, Bones helps Booth fix his plumbing. Booth presses against her hand as they connect a pipe and wait for the glue to dry. Booth says he is glad that they don't keep secrets from one another. They turn on the water which causes the pipe to burst.