A charred corpse is found in a metal shed that was set aflame. The shed – actually a fortified bunker – was filled with ammo, and the victim is wearing a fire-resistant vest. However, the vest wasn't bulletproof – the victim was shot before she was engulfed in flames. The victim is identified as Deanna Barbieri, former Marine sergeant, who was discharged a year ago after a fistfight with another Marine and had a history of misconduct, including assaulting an officer. Hodgins finds that the gunshot – which contained an illegal bolo – two bullets connected with a wire – is what caused the fire.
The first suspect is Carlene, the Marine she fought with, who was also discharged. Carlene reveals that Deanna believed that the world was headed towards an apocalypse. An old wound that seems to be from a homemade Civil War-style cannonball leads the Jeffersonian team to investigate the man who she purchased the lead from and the survivalist group of self-styled "doomsday preppers" to which he and Deanna belonged.
Meanwhile, Sweets, who is still living with Booth and Brennan, finds a new apartment, in a building with two other psychiatrists. However, Booth and Brennan are skeptical that he'll really be moving out.