Alicia and the children adjust to having Peter back home. At work, Alicia teams up with Diane to help a client testify against her wealthy husband in a murder case. Elsewhere, Peter sets to work on rebuilding his reputation.
Flashbacks reveal Finch's creation of the machine; Reese hits the road, leaving the team to deal with the aftermath of their war with HR.
After being reactivated to the NSA, Henry lies about it to Elizabeth; the office is impacted by Daisy and Matt's antagonism.
A recent loss creates a rift between Booth and Brennan, as they deal with their grief in different ways. Meanwhile, an old flame from Brennan’s past comes to visit.
Danny and Baez meet with resistance while investigating a bombing and Frank deals with political fallout after a man punches an aggressive officer.