On his way to pick up Brennan for an award ceremony, Booth is kidnapped and buried alive by The Gravedigger (the Season 2 villain who buried Brennan and Hodgins in the desert until they MacGyvered their way out). This time The Gravedigger wants evidence that's gone missing from the FBI. The FBI believes the evidence is with either Brennan or Hodgins looking to work the Gravedigger case freelance, or Thomas Vega, who had been writing a book about The Gravedigger.
Brennan deduces that Hodgins has the evidence, but he convinces her to withhold it and try to both get Booth back and unmask The Gravedigger. Meanwhile, you wouldn't expect Booth to take capture lying down, and he doesn't. He does everything he can to free himself, including hallucinating his dead spotter, Teddy Parker.
This episode has been pretty well panned online. The Gravedigger is apprehended before the final act break. Some wanted that storyline extended. I have to agree with others that Bones' portrayal of the military, both Seeley Booth's Rangers and Jared Booth's Navy, is not too accurate. But I think what's really bothering people is the woo-woo element in a show previously grounded in hard science.
Personally, I accepted Teddy as the personification of Booth's motivation to save himself. To show him working alone would have been less dramatic. What I had trouble with was Brennan's seeing Teddy at the end. I expected an ultra-rational person, who has never put her faith in anything supernatural, to see nothing.