With Sam still missing and all of 15 trying to find him, Detective Boyd tears into Andy, blaming her for blowing Sam's cover. Brennan just about knew she was a cop. Things get awkward when Luke finds out, considering his ex-fiancee seems to be responsible for screwing with Sam's undercover identity. Meanwhile a new rookie, Pete Sun, has joined the 15, and he's very eager to help out.
Brennan is torturing a tied-up Sam for information on what really happened to his wife and daughter. The official police report says that they died in a car wreck, but Brennan doesn't believe it for a second. He knows that this was a revenge move, but who masterminded it? Meanwhile Andy and Traci find out that the details on the report were removed, and the officer who ordered the changes was Detective Boyd.
Boyd seems more anxious than usual and when Traci asks about a boat called God's Good Grace, Boyd tries to shake her off that lead. Sam was using it as part of his cover, and it was seized in a drug raid. Brennan recognized the boat and that clued him in to Sam's true identity as a cop.
Luke finds out that Boyd has a gang informant who was involved with Brennan in the past. The gang member killed Brennan's family because Brennan murdered his brother. Boyd covered up the crime in exchange for the biker to offer up information about his gang.
The team finds a piece of property help in Brennan's wife's maiden name, and this is the place where Brennan is keeping Sam. Sam continues to provoke Brennan, who knocks him down so hard that his chair hits the floor. The chair breaks and Sam manages to free himself, and he and Brennan engage in a brawl. Sam seems to be on the losing side, but his fellow cops rescue him.
Andy gets orders to stay in the car with the newbie, Pete. She tells Pete about how things are probably going down in the house. After Sam is rescued, he and Andy are together, but they don't say anything to each other.
Afterwards, Dov invites Pete to the Penny to help celebrate Sam's rescue. Gail invites Luke to the Penny as well. The case involving Brennan's family has been officially reopened now that there's new evidence. Noelle informs Frank that she's pregnant.Sam and Andy have been suspended from the force for their actions, and they agree to try to live normally together for a while.