The episode starts out with Dr. Brennan waking up in a car. The radio is playing, but is very static-y. She can't get the car door open, so she tries rolling down the window. To her surprise, dirt starts to fall in the window. She quickly rolls it up. Suddenly, she hears a groan coming from the back of the car. She turns around to find an unconscious Hodgins. His legs are torn up and covered with blood. He has no idea what is going on and looks drugged. Brennan thinks that they have been taken by The Gravedigger.
48 hours earlier. Booth and Brennan are arriving at a crime scene where the cop thinks the bodies are aliens . They turn out to be two adolescent males. They had been there for years. Zack is reporting to Dr. Brennan about the bodies. He says that at least one of the boys bled out. He also says that they have extra foramina. Booth walks up and says he thinks this means they were twins. This turns out to be true and he has found the victims: Matthew and Ryan Kent. They went missing in 2001. No one ever found them.
Brennan and Booth are briefing a man and a woman about the remains in what is revealed to be a beer vat. They are introduced as AUSA Kim Kurland and ex-FBI Agent Pete Sanders. The two were the original agents assigned the case. They explain boys were abducted by a serial kidnapper called, "The Grave Digger." He abducts his victims and buries them underground. He then calls the loved ones and if they wire a certain amount of money into an offshore, untraceable bank account, he gives the family directions on how to free the victims. The Kent boys were the third victims out of six. Four victims paid the ransom and were saved. The Kent boys and one other didn't. The other victim was never found. The people they are briefing direct them to Thomas Vega, a kidnap and ransom expert. He has worked all but one of the Grave Digger cases. He works with a journalist. They tell him that the Grave Digger is never caught because he doesn't negotiate. He only makes one phone call and disguises his voice when doing so. Vega says that the abductor uses a stun gun to take the victims and that they don't remember anything.
Brennan and Zack are on the platform when Brennan notices "Bone Burn" made with over 300 degrees on Matthew. Oddly, the same mark doesn't appear on Ryan. Brennan sends Zack to get the medical reports of the other victims. Only moments after, Hodgins comes up and says that he found aluminum on the clothing of both boys, even though the vat was made of copper. Also, both boys' clothing was coated with engine exhausts from many engines, both gasoline and diesel. They deduce that the boys were taken from an underground parking lot and she asks him to compare his findings to the other victims. Brennan also wants to know how long the boys survived.
Brennan and Booth have a meeting with Mr. Kent, the father of the victims. Mr. Kent is very upset and blames the FBI for letting his sons die. Mr. Vega tells him to trust the FBI in this case: because they are looking for a killer now. He tells Booth and Brennan about his sons and how they were good kids. By now, Mr. Kent is blaming himself for his son's death. During the meeting, Brennan gets a text message from Hodgins. It says, "Victims did not have 24 hours of air. Only 12 hours max." She tells Mr. Kent about the new info and assures him that even if he had paid the ransom, his sons would've been dead before got there.
Brennan and Booth are in the car and she says, "Has it occurred to you that God is a lot like the Grave Digger?" This greatly shocks Booth, as he is an avid Catholic. She says that they both "lay down the rules, no way to question him or negotiate, then it's almost as if they don't care how it works out: either you do as he says, make some sacrifices and they are delivered, or you don't and you end up in hell." Booth tells her to stop and she asks to go to church with him. He tells her if she wants to do research, to turn on the religious channel.
Back at the lab, they discover that Ryan killed himself to give his brother more time. Cam explains that it'll mean something to their father that Ryan sacrificed himself.
On her way to karate class, Brennan is attacked and stunned by The Gravedigger. Hodgins, who ran down to find Brennan to tell her something important about the Grave Digger case, is hit by the Grave Digger's car. Brennan performs painful surgery on Hodgins to save his life and hotwires the car battery to her phone to send a text in less than 6 seconds to Booth. Booth receives the message and Cam, Zack and Angela try to help him decode the message. Meanwhile, the timer in the Jeffersonian lab tell the team that they have run out of oxygen. Booth tells the others that it's Bones and Hodgins and that they would find way to obtain more air. True to Booth's belief, Brennan cuts one of the tires to gain more air and Hodgins mixes two chemicals to create a carbon dioxide scrubber. Zack is able to decode the message using the periodic table and is able to pinpoint where Brennan and Hodgins are. Brennan then figures out a way to make the car airbag explode, which would either create enough force to help them out if they were less than four feet underground. If it was more than four feet, the explosion would turn their brains into jelly. Booth, the lab team and other FBI arrive to a digging site and stare at a large expanse of silt and dirt for possible areas where they could be buried. Underground and in their possible last moments, Brennan and Hodgins exchange tearful last words and ignite the explosion. Booth sees a poof of air rise from underground and runs toward it to help dig his friends out. Booth pulls Brennan out and the lab team rescue Hodgins.
Safe, Hodgins is found by Angela after he escaped from the hospital to the lab. He tells her that The Gravedigger buries people alive underground. Hodgins wants to stop him any way he can. He also admits to Angela that he can't sleep because he's afraid that if he closes his eyes, he will wake up in the car underground again. She tells him that he should come to her place, so when he wakes up, Hodgins will see Angela. Booth and Brennan are then seen in a church, where Booth is praying. Booth tells her that he thanked God for the entire team, that without them, they would not have been able to save Brennan and Hodgins.
- Temperance Brennan - Emily Deschanel
- Seeley Booth - David Boreanaz
- Jack Hodgins - T.J Thyne
- Angela Montenegro - Michaela Conlin
- Zack Addy - Eric Millegan
- Camille Saroyan - Tamara Taylor
- Assistant U.S. Attorney Kim Kurland - Salli Richardson-Whitfield
- Pete Sanders - Charles Mesure
- Thomas Vega - Benito Martinez
- Janine O'Connell - Julie Ann Emery
- James Kent - James McDonnell
- The Gravedigger - Deirdre Lovejoy (was not actually seen in episode)
- A Light On a Hill - Margot and The Nuclear So and So's
- Next to You - Tim Easton
- Never Know - Bob Gentry
- First episode to crown a "King of the Lab".
- Thomas Vega is portrayed by Benito Martinez in this episode, in his second and last appearance he is portrayed by Marco Sanchez.
- The Fox Network website initially displayed a summary for the episode which included an original ending where the Grave Digger was identified as Janine O'Connell, the female reporter that coauthored a book about Grave Digger and scenes to this effect were filmed. The summary was later revised to reflect the episode as broadcast in which the Grave Digger is unidentified and the scene replaced by character reunion moments.
- In this episode, Bones writes her final words. She reads them as her wedding vows to Booth when they get married.
- Instead of Dr. Brennan, Zack says "I don't know what that means" When Booth says "Zack, You're going to have to be Dr Brennan"—Which was probably intentionally ironic
The Woman in the Sand
The Headless Witch in the Woods
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