The Jeffersonian investigates the decomposing body of a social worker in the park, but evidence suggests the killer lived with the body for months before dumping it. Things get even more complicated when they determine another set of remains has similar details, which link the victims to a serial murderer who had sinister interactions with his victims' bodies. Booth and Aubrey consult with behavioral analyst Karen Delfs to help with clues to the killer's identity, while Cam tries to determine what (and who) she wants in her romantic life.

The team investigates the body of a private investigator who was found frozen in ice, after being dumped in the Potomac. The victim, a man with many enemies, was a "fixer" who made sure his clients' problems got "resolved." Meanwhile, Aubrey is shocked to find information tied to his father's whereabouts, Angela and Hodgins continue to work on their rocky relationship, Brennan and Booth get Christine's first report card and criminal behaviorist Karen Delfs asks Aubrey out on a date.

Booth and the rest of the lab desperately search for Brennan who was kidnapped by her former assistant, Zack Addy. Brennan's rescue is, however, just the beginning of their problems.

When a tutor of privileged students turns up dead, the team sorts through all the possible perpetrators, from disgruntled parents to the tutor's roommate with a criminal record. Meanwhile, Bones is frustrated with the voice of her audio book and tries to prove that she can record it herself.

Brennan testifies for Zach in trial, Angela reveals some big news, while Aubrey and Jessica come to terms about their future together. All the while, the team discovers Kovac has escaped, leaving Booth in a race against the clock to protect himself and those closest to him from what may be Kovac's most dangerous plan yet.

With Kovac still at large, the team searches for evidence to track him down. After Brennan experiences a setback, the rest of the team must figure out how to find Kovac without her, putting everything she has ever taught them to the test. When all signs point to Kovac having outside help, as well as a hideout, Booth and Brennan go searching for him.