Dr. Brennan is chatting on her computer with an unknown person when Goodman interrupts her with a top priority case involving the mafia: a member of the Cugini family was found in cement shoes. She makes a date with her chat buddy and gets to work. She is introduced to FBI agent Jamie Kenton who worked on the case undercover with the Ramano family for 2 years. Before she can get deep into the case however, Booth snags her away to another case deemed more important. A female body was found tied up and eaten by dogs.
Studying the second body, Brennan discovers that the eyes were gouged out and the throat was slashed, a fact obviously known by Booth first. Booth previously worked on a case involving another female found the same way (minus the dogs) and the case was unsolved because of insufficient evidence. The suspect was named Kevin Hollins. Brennan's date with David, her internet buddy, is moved up and she leaves the scene to meet him. While walking to the restaurant, she gets a call from him letting her know she is running late, then all of a sudden a car driving by takes a few shots at her, shattering the glass behind her. Luckily she isn't shot.
Brennan returns to the lab shaken up, but she tries to compose herself and continue on with her work. She berates Zack but apologizes for doing so. Booth arrives at the lab, worried about Brennan's safety. He does not want her to work either of the two cases she was presented for fear that someone does not want her to solve them. Brennan disputes that theory stating that the best way to save her is to find out who is behind the murders. She and Booth talk about suspects and Booth wants to include her date, which Brennan dismisses. Booth puts his foot down however and brings her date in.
In the interrogation room, Booth's questions get personal as he tries to discredit David. But he fails in his attempt, making Brennan like David even more, much to Booth's chagrin. At the lab, Angela makes a positive identification of the dead woman: Penny Hamilton, a 19-year old college student. Brennan knows that the information is going to upset Booth, who looks downtrodden when he sees the picture. Examining the body from the mob hit, Brennan thinks she might be able to reverse-engineer an imprint of the bullet using the indentations left on the bone. By doing that, Booth can track down the gun used in the killing. Zack reports that the blade used to slice the female victim's throat and the blade used to gouge out her eyes are two different knives. He was only able to match up the first blade - to a regular pocketknife.
Booth takes Brennan with him to the office to meet with Kenton and look over information he got while undercover with the Ramanos. But this is actually a ploy by Booth to scare Brennan off the case so she does not get hurt. She is unfazed and decides to continue with the investigation. Hodgins calls her to report that he found some liver with a parasite attached to it in the dog feces. Whoever starved the dogs lured them with the liver. And Zack found out that the pocketknife used on Penny has a nick in the blade.
Brennan and Booth visit the home of Kevin Hollins hoping to find the knife or the liver. He lets them in willingly and acts cooperative and curious. Brennan finds a knife lying in plain sight but it has no nicks. Hollins has a collection of keys in containers and Booth uses it to find some reason to bring him in. With his attorney present, Booth tries to scare Hollins into confessing, which includes showing him pictures of Penny's remains. Bones is watching through the one-way mirror and Kenton approaches with more information about the Ramanos. She informs him that she is trying to make a sketch of the bullet.
Booth doesn't have enough evidence to hold Hollins or the keys and consults Goodman's archeology skills for any insight he can give. Goodman reviews several pictures and points Booth in the direction of two containers of keys to focus on. None of the saw blades that Zack has tried compare to the cuts in the eyes because the cuts are of an irregular pattern. Hodgins approaches Brennan and Zack with the information that a compound found in the concrete used to sink Cugini led him to a company formerly owned by Carlo Ramano.
While trying to dig up information to use again Carlo in the interrogation room, Booth is informed that he has to give back all the keys to Hollins. In his ranting about losing a lead, he pushes Brennan to realize that the irregular pattern on the eye sockets could match the grooves of a key. She asks him to have the lab send an image of each key to Zack before turning them over to Hollins.
Booth accompanies Brennan to her home where he decides he will stay the night to keep her safe. With no television to watch, Booth raids her CD collection to find something likeable to listen to. Booth finds another side to Brennan as she has a diverse collection and finds a CD for them to dance to. He ends up playing "Hot Blooded" by Foreigner. A call from David interrupts their dancing session and Booth cuts the tension by going for a soda. While reaching for a cup, he opens the door to the refrigerator, and it explodes, blowing him back several feet. Reaching for the cup is the only thing that saves his life.
At the hospital, Brennan examines Booth's x-rays and gets information about his past from the past scars on his bones. They show that his feet were whipped with a pipe or hose which Bones knows is a common form of torture in the Middle East. She also sees signs that Booth at one time in his life spread his ribcage in a way that shows he was trying to protect someone. Booth assigns Kenton to protect her while he recovers from his injuries. At the lab, Angela is almost done making an imprint of the bullet, a process that Kenton is very interested in. Hodgins' examination of the explosion from Brennan's apartment shows a chemical isotope that leads straight to Hollins. An FBI raid of his apartment reveals a map and several more keys. Zack calls to tell Brennan that Hollins never picked up the keys and they found the one that removed Penny's eye, but there were no substances on the key to trace.
Hodgins informs Booth of the progress so far when he visits him in the hospital. Booth puts several pieces together and deduces (with Hodgins' help) that the mob framed Hollins for the explosion in Brennan's apartment to throw off the investigation. But the only way they could do that is if someone in the lab is working for the mob. Booth needs to leave the hospital to pursue leads.
While driving to the lab, Brennan informs Kenton that she is ready to find the bullet that killed the mafia member when she gets there. He then kidnaps her at gunpoint and takes her to a warehouse where he plans on killing her and making it look like Hollins killed her. She manages to fight back some but he gets the upper hand and subdues her. Booth manages to track her down and the FBI raids the building, searching for signs of her. Booth finds her and shoots Kenton before he can kill her. They share an embrace as Booth removes her from the hook she's hanging from. Afterwards in the hospital, Brennan is ready to go on her date with David, but cancels it to spend time with Booth in his room watching TV.