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 other detectives. Bones then gets a call from the Gravedigger who tells her that he has taken Booth and buried him alive. He tells Bones to use a GPS to locate him. He says if she involves law enforcement, he 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 police help. Sweets says they can't call them 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 Parker must be a hallucination because he's dead. The two argue briefly and Booth tells Parker he is going to focus on what is real.

Bones asks Hodgins if he has the Gravedigger evidence. She says the Gravedigger thinks she has the evidence, but he'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 FBI. Bones then scolds Hodgins for stealing evidence. Hodgins says it was the only way he could solve the case. Hodgins asks for a ten hours to study the evidence, then he'll turn it over. Bones agrees to eight.

Angela analyzes the Gravedigger's call and compares it to 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 Booth must be near the water.

Booth tries to escape from the room he is being held in. He accidentally opens up a pipe that sends water pouring into the room.

Bones tells the team that Booth is 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 detectives 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. Parker goes into the water and retrieves a pry bar. Booth uses the bar to open a door. Booth and Parker walk through the door and find another room. Booth tells Parker 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. Parker instructs Booth on how to pick the lock. Parker asks Booth if he has any kids and Booth tells him he has a son named Parker. Booth tells Parker about his son and his son's mom. Booth then looks out a window and realizes he's on a ship. Parker points out that she ship is wired with explosives.