Here’s the official Bones Season 7 Finale synopsis from Fox:
Evil tech genius Christopher Pelant (guest star Andrew Leeds), a suspect in a previous case Brennan and Booth handled, is back in court on appeal. Knowing what he is capable of, Brennan and Booth inform the judge that he is a suspect in two murder cases. Then, Brennan and Booth are called to the scene of a new murder. After determining the victim is Brennan’s friend, who also is linked to Pelant, the Jeffersonian team works to prove he is guilty once and for all. But when law enforcement examines the team’s findings, key pieces of evidence are tied to Brennan and suspicion falls on her.
Brennan’s a suspect in a Jeffersonian investigation? Talk about conflict of interest. If the latest batch of spoiler photos tell us anything, it’s that Booth is going to yell into cell phones and shake the lapels of everyone he can until Brennan’s name is cleared.