The evidence from the Gravedigger case has gone missing. Brennan and Hodgins, who have not fully recovered from being buried alive, are suspected of taking it. On the night of a ceremony recognizing Brennan, Booth gets knocked out, tasered, pumped full of drugs, and stuffed in a toy-like yellow submarine. When he gets out of the tiny submarine, Booth finds himself face to face with someone from his military past. The team works on locating Booth and finding who is behind the kidnapping, with the help of Booth's brother Jared.
Bones, Hodgins and Vega are called to meet with Judge Williams to discuss the Gravedigger case. AUSA Heather Taffet tells the detectives that some evidence has gone missing. The detectives are told that if they have the evidence and turn it over today, they will get full immunity.
Bones calls Booth and asks if he needs directions to a ceremony. He assures her he's fine. Bones arrives at the headquarters and gathers the others. Bones then gets a call from the Gravedigger who tells her that she has taken Booth and buried him alive. She tells Bones to use a GPS to locate him. The Gravedigger says if Bones involves law enforcement, she will know and Booth will die.
Booth finds himself in a holding cell. He uses the glow of his watch to create light. The team goes to Booth's apartment to look for clues. Bones sees that Booth was dragged out through his window. Angela says they need the police's help. Sweets says they can't call them (the police) if they want to get Booth back.
Booth pounds on his holding cell walls. He sees a bolt on the ceiling and unscrews the nut. He is able to expose a small hole that he can see out. Booth then unscrews another nut and is able to climb out of his holding tank. Booth calls out the the darkness. Teddy Parker emerges and Booth asks if he's real. Booth says he's been drugged and Teddy must be a hallucination because he's dead. The two argue briefly and Booth tells Teddy he is going to focus on what is real.
Bones asks Hodgins if he has the Gravedigger evidence. He says the Gravedigger thinks she has the evidence, but she's wrong. Hodgins unveils the evidence, including material that was embedded in his leg when the Gravedigger ran him over. Sweets arrives and Bones tells him he can't help since he's part of the FBI. Bones then scolds Hodgins for stealing evidence. Hodgins says it was the only way he could solve the case. Hodgins asks for 10 hours to study the evidence, then he'll turn it over. Bones agrees to eight.
Angela analyses the Gravedigger's call and compares it with an earlier call. She says she can't unscramble the voice concealer, but she can isolate background noises. Angela tries to assure Bones that they will get Booth back. Angela then hears the background noise is birds. Bones says they sound like seagulls, and so Booth must be near the water.
Booth tries to escape from the room in which he is being held. He accidentally opens up a pipe that sends water pouring into the room.
Bones tells the team that Booth must be near the ocean. Bones figures that based on Booth's GPS location, he might be near the boardwalk. Hodgins remembers that Vega lives near the boardwalk. The team then finds Vega dead inside his car. They figure the Gravedigger killed Vega somewhere else then moved him to his car. Hodgins suggest they move Vega back to the lab to look for evidence. Bones says they shouldn't move the body. Agent Payton Perotta then arrives and tells the two to step away from the car. Perotta admits that she was following Bones and Hodgins since they are suspected of stealing the evidence. Hodgins suggests that Vega was the one who stole the evidence since he's dead.
The water fills up the room, but Booth is able to climb to a catwalk. Booth looks for another way out. Teddy goes into the water and retrieves a pry bar. Booth uses the bar to open a door. Booth and Teddy walk through the door and find another room. Booth tells Teddy he must be a ghost since he was able to help him. Booth then looks around the room and sees he is locked in a cage. Teddy instructs Booth on how to pick the lock. Teddy asks Booth if he has any kids and Booth tells him he has a son named Parker, named after him. Booth tells Teddy about his son and his son's mom. Booth then looks out a window and realises he's on a ship. Teddy points out that the ship is wired with explosives.
Bones and Hodgins tell rest of the team about Perotta. Bones says they are going to turn over the evidence to the Gravedigger. The team arrives at the drop off point. Sweets points out the video camera that the Gravedigger is using to confirm that they are dropping off the evidence. Sweets and Angela monitor the video while Hodgins and Bones put the evidence on the grave. Sweets and Angela see that the Gravedigger is nearby. Angela realises the signal that they have is not coming from the camera. Angela tells Hodgins and Bones to get back. They start to run and the grave site explodes.
The team tell Judge Williams about the evidence and the explosion. He instructs Perotta to bar them from the case. The team returns to their headquarters. Hodgins thinks it's over, but Bones says she has an idea.
Booth wonders why the boat is stuffed with toys and explosives. Teddy tells him that it is common to sink ships and use them as reefs for fish. Teddy says they are often decorated by children.
Bones calls Booth's brother Jared to help find Booth. She asks him to steal Vega's body so they can study it for evidence. Jared says he can't steal the body from the FBI. Bones tells him his brother never turned his back on him, and Jared decides to help.
Booth flashes back to when Teddy was killed. He tells Teddy he shouldn't gone on the mission because it was beyond his abilities. Teddy asks Booth about his partner, and Booth says he would like her. Booth then wires the explosives to try to send out a signal. He shorts it out and breaks it. Teddy tells Booth that there is now no way to stop the explosion. Teddy says the only way to escape is to jump into the ocean. Teddy says if Booth dies, he dies too since no one else remembers him. Booth tells Teddy that Claire goes to his grave every year on the anniversary of his death. Teddy then asks Booth to tell Claire he loves her since he never got the chance. Teddy then suggests that he is there because Booth has someone that he never told he loved them.
Jared brings in Vega's body. The detectives study the body and find burns marks from a stun gun. Bones says the injuries are different from the other deaths. They find that Vega fought back and probably did damage to his attacker like breaking his ribs.
Teddy fashions some plastique explosives in the shape of a mermaid. Booth puts it on a wall and asks for a power source. Teddy hands him the flashlight.
Taffet walks in to the headquarters and orders the detectives to hand over Vega's body. Bones asks for a warrant, and Taffet hands it over. Bones decides to tell Taffet about contacting the Gravedigger. Bones then notices that Taffet can't extend her arm. She whispers to Hodgins, and he suggests it's possible that she could be the Gravedigger. Bones then pushes Taffet in the ribs, and she crumples in pain. The team then realizes she is the Gravedigger.
Hodgins tells the team that Taffet won't talk, and they need to figure out a way to get her to open up. Hodgins tells Taffet he wants to kill her. Jared then tells Taffet that he went through her files. He says he knows she created a false identity to rent a storage locker.
Booth nervously starts to connect the wires. Teddy runs away in fear. Booth uses a pipe to push the connections together. Teddy decides to do it for him, and the wall explodes. Booth says the explosion affected his vision. Teddy says he needs help. Booth picks Teddy up and helps him toward the hole. Booth then relives Teddy's death. Teddy tells Booth that he ignored his order, and his death was not his fault.
The team suggest that they torture Taffet to get the truth, but Sweets tells them they can't. Angela tells the team they have the contents from Taffet's storage locker. Hodgins finds a mosquito and paint chips. Hodgins says the paint is an obsolete paint used for navy vessels. Angela remembers hearing about an old Navy ship that was being prepared to be sunk. Angela then tells Bones she knows where Booth is. Bones gets up, picks up a nearby suitcase, and smacks Taffet, knocking her down.
Jared calls Bones on the helicopter and tells her that they can't stop the explosion. Meanwhile, Booth gets out to the ship's deck. Teddy thanks Booth for carrying him so far. Bones sees Booth and calls him over to the helicopter. Booth hesitates as he leaves Teddy behind. The helicopter takes off and the ship explodes.
The next day, Bones accompanies Booth to Teddy's grave. Booth thanks her for saving his life. Bones says she read his report and thinks it would have taken two people to accomplish what he did. Booth says he had a ghost help him. Booth tells Bones about Teddy. Booth then sees Claire, and he tells Bones he needs to give her a message from Teddy. Bones watches Booth hug Claire. Teddy then walks by Bones, telling her it's a beautiful day to be alive. Bones agrees, oblivious of who just talked to her.
- Temperance Brennan - Emily Deschanel
- Seeley Booth - David Boreanaz
- Jack Hodgins - T.J Thyne
- Angela Montenegro - Michaela Conlin
- Camille Saroyan - Tamara Taylor
- Lance Sweets - John Francis Daley
- Thomas Vega - Marco Sanchez
- Jared Booth - Brendan Fehr
- Payton Perotta - Marisa Coughlan
- Heather Taffet - Diedre Lovejoy
- "When The Pain Dies Down" - Chris Stills
- Parker, Booth's son, is discovered to be named after Teddy Parker.
- Thomas Vega is portrayed by Marco Sanchez in this episode, however the character's first appearance in the series, he is portrayed by Benito Martinez.
- While incarcerated in the hold, Booth hallucinates that his 'spotter' from his sniper days, a young man named Teddy Parker who died after saving Booth, is helping him escape. In fact, several doors on the ship could not have been opened without the help of a second person, and Bones is seen talking to him at the site of his grave, with Bones unaware of his identity. This is one of a handful of episodes that suggests the existence of paranormal entities.
- The footwear worn by Teddy Parker as he speaks to Bones in his Class A uniform is incorrect. Paratroopers, Rangers, and Special Forces Soldiers all wear boots similar to the ones worn by WWII-era Paratroopers as opposed to Oxfords in their dress uniforms.
Booth was visited by the ghost of Teddy who helped him escape and asked him to deliver a message to Claire. Also, he wanted to tell Booth he wasn't guilty of his death.
- "You ain't ever love somebody and not tell em?" - Teddy Parker. He says this to Booth when he criticizes that Parker never told his girlfriend that he loved her
Fire in the Ice
The Princess and the Pear
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