"Hero in the Hold" is episode fourteen of season four of Bones, the forensic drama television series loosely based on the novels and life of anthropologist Kathy Reichs. In this episode, Booth is kidnapped by the Grave Digger.
In "Aliens in a Space Ship", Brennan and Hodgins were buried in a car by a killer/kidnapper called the Grave Digger, who would kidnap his victims and bury them alive until a ransom was paid. Although they managed to escape, the Grave Digger was never caught. Or even identified (there were a couple of potential suspects, at least from the viewer's point of view, who were connected with the case).
This episode opens with Brennan, Hodgins and former FBI Special Agent Vega in front of a judge. Apparently, some evidence has gone missing from the FBI connected to the Grave Digger case. There's a new person in charge of the case - the previous one having died in a car accident a month ago - and she wants it back.
Booth is Kidnapped
That evening, Brennan is talking to Booth on the phone - they're going to a special event for her - when he gets a knock on the door and hangs up. As Brennan and the others are about to leave the Jeffersonian, she gets a call - from the Grave Digger. He's caught and buried Booth, and the latter has less that a day's worth of air. The Grave Digger wants the stolen evidence. They can't involve the authorities.
Hodgins Has the Evidence
Hodgins actually stole it; it's the piece of car that was in his leg. He's getting close to identifying the make and model, which would help catch the killer. So Hodgins asks if they can spend some time trying to identify it before handing the evidence over, and Brennan agrees to ten hours.
No Such Thing as Coincidence?
Now, it seems a bit of a coincidence for the Grave Digger to demand the stolen evidence just after several people have been told it's been stolen. Vega was one of the potential suspects from the previous episode, the other being the woman who died in the car accident, and some more evidence quickly points to him. He is, however, rather dead, so now both of the potential suspects are dead. Hodgins wants to take the remains to the lab, but Special Agent Perotta and the FBI arrive on the scene. Hodgins and Brennan were being watched by the FBI, because they were suspected of taking evidence. As Hodgins points out, if they were watching Vega as well, they didn't exactly do a bang up job.
Seeking Help from Jared
The Grave Digger doesn't actually want to free Booth. He seems to be cleaning up evidence leading to him - which includes Booth. So Brennan reaches out to Booth's younger brother, Jared, for help.
Booth is Running Out of Time
Booth manages to escape from the metal container he's in, but that only leads out into a larger metal room. When he tries to get out, water rushes in. He's also seeing a dead person from his Army days - Parker (he hallucinated in the previous episode, "Fire in the Ice", as well. Although Booth decides that this one is a ghost). Booth is actually in the hold of a ship, rather than underground. One that's rigged to blow. And then sink.
It's a definite race against time to save Booth.