Air date: 3/28/07

Brennan and Zack examine corpses, which have been spilled out of their coffins, due to a burst water main in an old cemetery on the St. Agatha church grounds. However, as they identify the individual bodies to be put back in their proper place, they find one skeleton that is out of place. Father Donlan, who runs the church, says all these bodies had been buried for at least 50 years and yet Brennan believes one of them was buried five years ago with no coffin. When it is confirmed the deceased was murdered, Booth and Brennan investigate the priests and administrator of the church and argue about the validity of religion.

The Killer in the Concrete

Air date: 4/4/07

The remains of a body are discovered encased in concrete, and Booth has a hunch the victim is connected to an organized-crime boss. Meanwhile, Brennan's estranged father pays her a visit.

Spaceman in a Crater

Air date: 5/2/07

The team investigates the death of an astronaut who appears to have fallen to Earth from a high altitude. While Brennan and Booth question his associates at the Space Agency, Hodgins theorizes about a conspiracy involving extraterrestrials. Hodgins asks Angela to marry him but she refuses, asking him to keep trying.

The Glowing Bones in the Old Stone House

Air date: 5/9/07

Brennan and Booth are called by Homeland Security to investigate the scene at an old stone house where some glowing bones have been found. Fearing the remains might be radioactive, the pair don protective hazmat suits and cautiously enter the house, where they find the glowing bones but no radioactivity. Back at the Jeffersonian, the team examines the bones and determines the identity of the victim, but there is no immediate explanation as to why the remains are emitting a green glow. With each of their specialties called upon, the whole Jeffersonian team joins Brennan and Booth in pursuing the murder mystery, which leads them to a group of friends who are shocked to discover one of their own is the victim. During the course of the investigation, the victim and their friends' MySpace pages, along with the photos, videos and blogs they contain, are a virtual tool for the Jeffersonian team's search for answers. Meanwhile, Hodgins professes his love for Angela in a very unusual way. In the end, Angela decides to propose to Hodgins and they agree to get married.