When a commuter jet crashes, the Jeffersonian team is charged with identifying the remains of several Chinese diplomats. Brennan however is more interested in other remains found at the site, and she is encouraged to investigate them after a man shows up at the Jeffersonian convinced the remains belong to his missing father. 

The remains of a young documentary filmmaker are found in a ventilation shaft in an underground Washington, DC, tunnel. The investigation leads the team to a society living in the tunnels and a lost treasure of American art.