Bones

The episode opens with Booth, Brennan, and Zack being lowered down an access shaft into an underground tunnel system. They have been called in to investigate a body found at the bottom of another access shaft. When they arrive, the remains are being eaten by rats. Brennan borrows Booth's weapon and shoots a rat so the other rats will feed on it and leave the body alone. Brennan finds that the victim is female and many of her bones were shattered as a result of falling from somewhere up in the access shaft.
Booth notices that the victim is not wearing shoes or a jacket. As Booth is making this observation, Brennan notices a man lurking in the shadows, watching them. She calls out to the man and he runs away. Brennan begins to run after him, but Booth stops her, reminding her that it is not safe to go running after strange men in the dark. Brennan notes that the man didn't need a flashlight to navigate the dark tunnel system, and concludes that he must be very familiar with the surroundings.

Once the remains are brought to the lab, Brennan is able to identify the victim through the serial number of a surgical pin implanted in her knee. The victim is Marni Hunter; a documentary filmmaker reported missing by her fiancé ten days ago. Based on insect activity, Hodgins also places time of death at ten days ago. Brennan is unable to conclusively determine cause of death based on her observations so far. She determines that the victim fell approximately 40 feet, landing feet first and crushing her tibias, but the victim also sustained skull injuries that were not the result of landing on the tunnel floor. The forensics team found blood and bone fragments on several pieces of pipe protruding from the walls of the access shaft, so these could have accounted for the skull injuries, but as the victim's fingernails show no signs of clawing at the walls to slow down her fall, it is clear she was either dead or unconscious when she fell.

Brennan and Booth first interview Marni's fiancé, Phil, in Booth's office. Booth questions why it took Phil two days to report Marni missing, but Phil explains that it is not unusual for Marni to get caught up in her work as a filmmaker and disappear for a few days. He tells Brennan and Booth that Marni's latest project was a documentary about the community of homeless people who have set up an underground city of sorts in the tunnels. Booth inquires about Marni's coworkers, but Phil tells him that Marni always worked alone and never appeared on camera. He has brought along the footage that Marni had pieced together so far. Brennan recognizes one of the homeless men featured in the film as the man she saw running away from the crime scene. Phil does not recognize the man, but is able to identify the woman he's talking to as a social worker named Helen who works at a homeless shelter on 26th Street.

Brennan and Booth track down Helen the social worker and she takes them down into the tunnels to find the man from the crime scene, whose name is Harold. Helen explains that she wasn't a fan of Marni's work because she found it exploitive and in violation of the homeless community's right to privacy. However, as far as she knew, Harold and the rest of the community seemed to like Marni. Harold is hostile at first, until Brennan reminds Booth that Harold is a person of status in his society and should be treated as such. Once Booth respectfully asks Harold for his help, Harold tells the partners that he was at the crime scene to check on Marni. Booth then finds Marni's video camera and a pile of bloody clothing with Harold's belongings, so he cuffs him and brings him back to the FBI building.

In the interrogation room, Harold is bothered by the brightness of the sunlight coming in through the window, having spent so long in the dark tunnels. Booth talks to Harold about his military background, and Harold admits that he became a recluse after a traumatic incident during his time in the military, when he was forced to shoot a pregnant woman holding a grenade in one hand and a child in the other. The actions saved the lives of Harold and the other men in his unit but resulted in the deaths of the woman and her child, and Harold never recovered from the guilt of that. Harold reiterates that he came upon the crime scene after going looking for Marni, worried for her safety after not having seen her in a few days. He admits to taking her jacket, shoes, and video camera to sell, but insists Marni would have wanted him to have her things. Harold does say that he "gave her something, and that's why she died", but, distressed by the brightness of the room and advised by his lawyer not to say any more, he refuses to give any further details on what he gave Marni or how it resulted in her death.

Meanwhile, Brennan reconstructs the victim's skull from the shattered fragments, and Zack is able to determine that the head trauma they previously thought may have been caused by striking her head on the way down the access shaft was actually the result of a blow from a sharp weapon.
Amongst the victim's possessions, Hodgins finds a medallion that Goodman identifies as an official War Office vault seal. Goodman tells Brennan and Booth that beginning in the late 18th century, several underground vaults were built to safeguard cultural treasures-currency, paintings, engravings, etc.-and that a few were unaccounted for after a series of cave-ins blocked access to the tunnels. Goodman believes the seal came from one of the previously undiscovered vaults, and if so the items within would be extremely valuable.

Brennan and Booth interrogate Harold again, and he admits that the vault seal is the item he gave Marni that he believes got her killed. Harold is again cryptic when Booth asks him where he got the seal, saying he got it "beyond the perimeter" and took it from "the blond". Brennan asks Harold to take them to where he found the seal, but he refuses, saying he took Marni beyond the perimeter and doesn't want to make the same mistake again.

Brennan and Booth then go to interview Helen the social worker again, since she is blond. On the way, Brennan receives a call from Hodgins, who tells her that, based on diamond dust found on Marni's clothing, she was killed in a 19th century tunnel system, much older than the tunnel she was found in. When questioned, Helen denies being the blond that Harold spoke of. She also tells Brennan and Booth that Marni took climbing lessons from a couple of local guys to learn how to use ropes to climb down into the tunnels.

Back at the Jeffersonian, Angela feeds the details of the head wound into the Angelator and runs a simulation of the attack. She determines that Marni was struck only once, with a glancing blow that was nevertheless fatal, and that the killer was left-handed.

Using Marni's credit card records, Booth is able to track down the instructors who gave her climbing lessons, and he and Brennan go to question them. The two men, Kyle and Duke, tell Brennan and Booth that they gave Marni a few lessons, but not nearly enough for her to try going down into the tunnels alone, and they had never gone in with her. Kyle seems particularly upset about the news of Marni's death, and Booth guesses, correctly, that he and Marni's relationship was intimate. Kyle admits to the affair but says they had a mutual breakup because Marni was engaged and he had no interest in getting married.

With this new information, Booth questions Marni's fiancé Phil again. Phil says he knew Marni was involved with another man, but he didn't know who the other man was, and that the affair was over before Marni died. He also admits that this was not the first time that Marni had cheated on him, and that their wedding had in fact been called off. However, despite his newly-discovered motive, Phil still insists he had nothing to do with Marni's death.

Brennan and Booth appeal to Harold once again to lead them to where he found the vault seal, and he finally agrees that he will bring them just to the "perimeter" and point them the rest of the way. When they reach the tunnel Harold leads them to, they do not find the War Office vault, but they find a set of completely skeletonized remains with a bullet hole in the skull. Once the remains are brought back to the lab, the Jeffersonian team determines that they date back to the Civil War era.

Next, Angela meets with Harold to do a sketch of "the blond" while Zack makes a cast of Marni's head wound to try to determine the murder weapon. Meanwhile, Marni's fiancé discovers some raw footage Marni took in the days before her death and brings it to Booth. Brennan and Booth watch the footage and discover that while Marni started out to make a documentary on the homeless, she had turned her attentions to trying to find the fabled vault of treasure. The footage also shows Marni's climbing instructors, Kyle and Duke, operating the camera, despite the fact that they told Brennan and Booth they had never gone down into the tunnels with Marni.

Unfortunately, Kyle and Duke are now nowhere to be found, so Brennan and Booth can't question them again. Brennan and Zack hypothesize that the murder weapon was a climbing ax, further indicating the climbing instructors as the culprits. Angela returns disappointed from her sketching session with Harold; she shows the others her sketch, which looks like an old-fashioned portrait. Dr. Goodman, however, recognizes the woman in the sketch as the subject of a long-lost painting by Sir Henry Raeburn, now worth over $200,000. The painting is exactly the sort of thing that is likely to be in the War Office vault, so if Harold saw it, then he must have seen the inside of the vault at some point.

Booth realizes that Kyle and Duke are probably emptying the vault as they speak and wants to rush in to find them, but Brennan reminds him that he is unlikely to find them in the labyrinthine tunnel system. Using the Angelator, Angela brings up a schematic view of the tunnel system, including very accurate renderings of modern utility tunnels as well as less accurate depictions of historical tunnels from old maps and written accounts. The team knows the treasure has to be in one of the historical tunnels, so they eliminate the modern utility tunnels from the diagram. They are able to further narrow down their options by taking into account the diamond dust that was found both on Marni's body and the Civil War skeleton. By adding in the discovery sites of Marni's body and the soldier's body and connecting the two points, they are able to create a path along which they hope to find the vault.

Using Angela's map, Brennan and Booth descend into the tunnels and locate the vault. They find Kyle and Duke inside, packing the treasure into bags. They are unarmed, but when Brennan explains that the evidence says whichever of them is left-handed killed Marni, Kyle seizes a candlestick and hits Duke over the head for murdering his girlfriend. Duke survives the encounter, and it is later revealed in interrogation that he killed Marni because she only wanted to document the treasure, while he and Kyle wanted to take it for themselves. The real killer apprehended, Harold is released from custody, and Brennan, Booth, and Angela accompany him back to the tunnels and give him the vault seal to keep.