The episode begins with Christopher Pelant sitting in front of surveillance monitors. He seems to be surveying the entire city. One of his monitors begins to beep and Pelant enhances the image on that screen; it is Brennan. At home, Booth and Brennan discuss marriage. Brennan tells him that she loves him, but she isn’t sure about marriage. Booth gets a call about their latest victim. The duo arrives at the crime scene. The remains are found in a trail that has been closed for two months. Cam tells Booth that the trail was re-opened today and that is when the rangers found the remains.
Hodgins checks the larvae and says that the victim has been dead for five days. There are multiple gun shots, indicating that it was a murder. Brennan declares that the victim is a Caucasian male in his fifties. Cam points out that at least one shot was taken at the picnic table because there is blood on the table. Brennan states that the first shot could have killed the victim. She feels that the remaining shots were clearly unnecessary. At the lab, they identify 12 bullet wounds. Brennan looks at the bone x-rays and states that the bone remodeling shows two gunshot injuries that are approximately 8-10 years old. So, this is not the first time the victim had been shot.
At the FBI office, Booth and Sweets talk about the case. Booth tells Sweets that the killer used the regular 9mm. Sweets tells him that there is no evidence that the victim was eating at the table, which means the victim was lured there somehow. Sweets feels that the body was left there intentionally, so that they could find it. They doubt it could be Pelant. Angela video conferences with Booth and tells him that she got a hit on their victim. It is Alan Friedlander, a retired cop. Booth tells Angela that Alan and he were partners when he first started out. Later, Booth briefs his team about Alan’s murder. At the lab, they find a lot of puncture wounds on the bones which look like dog bites.
Brennan checks Alan’s medical records. There is no evidence of bites or gunshot wounds from ten years ago. They feel that the records could have been altered. At the FBI office, Sweets shows Booth a paper that he wrote a while back. He tells him to check the highlighted area. This murder took place exactly how it is described in his paper. Sweets adds that this paper wasn’t published. He feels that Pelant hacked into his computer. At that moment, Booth gets a call; another agent is found dead. This time there is a witness. The girl tells Booth that the man, who knocked her down, was wearing a hat and he had a tattoo on his hand. The cops also find a ski hat in the trash.
Booth receives a call from Pelant, where Pelant tells Booth that he is not going to find him. Pelant tells Booth that he crossed a line when he shot him. At the lab, the team finds out that Stone, the latest victim, has bite marks on his bones. These injuries are from ten years ago, just like Friedlander’s. Cam states that Stone’s medical records have been wiped clean. Cam and Angela think that Booth should walk out of this case because Pelant is targeting FBI agents. Booth’s life could be at risk. Brennan tells them that Booth is the best and he has to catch Pelant. At the office, Booth and Caroline talk about Crystal Creek, a cult ground, where Stone and Friedlander were attacked by their guard dogs.
Caroline wonders why it isn’t mentioned in their files. Booth tells them that the raid was a part of some secret ops and their files were moved to a secure location. He too was a part of that team. Sweets arrives and tells them that Pelant is using his work against them. He feels that Pelant is working through a surrogate because a number of children saw their parents getting killed during the raid. At the lab, Brennan is upset that Booth did not mention Crystal Creek to her. She fears that Pelant will kill Booth. Booth assures her that nothing of that sort will happen.
At the lab, Sweets manages to narrow down the name of a potential surrogate, an FBI blogger whose parents were killed in the compound raid. Booth and the SWAT team manage to arrest Zane, the surrogate. During their interrogation however, they learn Zane wasn't the one who killed Stone and Friedlander. Moreover, his alibi checks out. Booth gets a call from Brennan and he rushes to meet her. She hands him a packet of beef jerky because he loves it. She then cries and asks him if he would marry her. She says that all this has made her see things clearly and she wants him to be her husband. Booth is happy and he says yes.
They hug, completely unaware that Pelant is watching them. At the lab, Brennan tells Cam that Friedlander was shot just 11 times. One of the bullets got separated inside the body, creating two exit wounds. So, now Friedlander and Stone were shot 11 times. They wonder what could be the connection between FBI, Crystal Creek and 11. Booth tells Sweets that Brennan asked him to marry her. Sweets is happy, but also worried. He feels that Pelant would feel that he is being replaced, and that this could cause him to escalate. At the lab, Angela tells Brennan that they have been looking in the wrong place. She tells her that the surrogate is Anna, the daughter of one of the agents, Harris Samuel, who was killed during the raid. He was shot 11 times. By the age of 10, Anna was trained to be an expert marksman. It now makes sense.
At home, Anna is watching a video where her father gives her instructions to kill. The video is actually made by Pelant. He used some computer tricks to replace his face and voice, with Samuel’s. It is also seen that Anna is the witness, who Booth met in the park. Anna calls Booth and tells him that she needs to talk to him right away. Brennan calls Caroline because she is unable to get through to Booth’s phone. It looks like Pelant has jammed all the signals. She tells Caroline about Anna Samuels. One of the officers pulls up the records and tells Caroline that Booth has gone to meet her because she is their witness from Stone’s crime scene and she called herself Allison Taylor.
Brennan asks for Sweets, and Caroline tells her that Sweets too has gone to help Booth with the questioning. The FBI barges into Anna’s house and helps Angela to gain access to her computer. Angela finds the weird video sent by Samuel. They figure out that it is Pelant’s doing. They also decode an encryption on that file which says “BOOTH DECOY SWEETS TARGET”. This means that Anna is going to kill Sweets, who is stuck in a traffic jam created by Pelant. Booth calls Brennan from a pay phone and Brennan tells him about their recent findings. She also tells him that Sweets is the target. Booth rushes to save his friend. Brennan also rushes to check on Booth. Booth runs through streets, over the idle cars caught in the traffic jam, and spots Anna. Anna spots Sweets and pulls out her gun.
Before Anna can pull the trigger, Booth shoots her in the shoulder. Brennan is relieved to see that Booth is all right. At the FBI office, Caroline wants Sweets to get information out of Anna. Booth spends time with Brennan and Christine in the park. At that moment, he receives a call from Pelant. Pelant tells Booth that he should tell Brennan that he will not marry her. Pelant, who is watching them at the park, tells Booth that he cannot tell Brennan the reason why he doesn’t want to marry her. Pelant threatens to kill five innocent people present in the park if Booth ignores him. Booth whispers to him that he will kill him and hangs up the phone. Later, at home, Booth tells Brennan that he cannot marry her. Brennan is hurt, but she says that she understands. She gets up and goes upstairs. The episode ends.