Episode 16 of "Bones"
s01e16 The Woman in the Tunnel

When the remains of a young documentary filmmaker are found in a ventilation shaft in an underground Washington, DC, tunnel, Brennan and Booth must venture into the maze of tunnels beneath the city and are surprised to discover a world of homeless shelters underground. Clues lead them to suspect that a man living underground was involved with the murder, but instead he gives them valuable information about the purpose of the victim’s underground project. When a valuable artifact is found among the victim’s possessions, the entire Jeffersonian team joins in the investigation to learn why the victim was in the maze of tunnels and what she found down there that led to her murder.