The episode begins with Neal still giving Peter the cold shoulder, as he is still hurt and has decided to keep only a professional relationship with him, from here on end. The two meet at the FBI's Best Practices conference, where Peter is being featured as a one of the better handlers. It's a big deal for him, from the look of things. During the panel things get a little awkward as Neal seems to be trying to embarrass Peter, as he is clearly angry at him. Just then, a security breach is reported and the panel has to be rescheduled as a result. The panel shall instead be held the following day. Peter tags along with the agents to investigate, and to get to the bottom of the matter.
Neal comes home to find Mozzie with Sam, much to his surprise. Neither will tell the other his name but eventually they make nice. The three come up with a plan to flush out whoever has access to the FBI files. The plan is to put Sam's name out there, but under their terms, so they can bait the person involved. Peter reports to his team that the security breach was carried by somebody who cloned an agent's badge, perhaps to steal some of the high-tech equipments being exhibited in the conference. The plan is to target the highest-attended panels. At the identity theft panel Neal pretends to steal a badge while Jones video tapes the room. Peter asks one of the agents named Furlong about Sam, and tries to find out if he has any leads about Sam that might be useful.
Later at home, Peter tells Elizabeth he thinks Sam could have handled things better before leaving town, if he really wanted to. On the other hand, the plan is for the guys to lure out whoever is tracking Sam, and then try to plant a monitoring device on them, so they can keep a track of the person’s movements. Neal is going to fill out a surveillance authorization form on Peter's behalf, so they can put their plan in place. Neal uses Mozzie's pet rat to distract Peter and in the end gets him to sign the form himself. Using facial recognition the team finds out that, a former military man named Anderson is the one infiltrating the conference. He's now working security and is involved in espionage, and hence he is doing whatever he doing. The plan is to follow him without spooking him, so they can find out who he really he working for and then eventually catch him red-handed.
Peter finds out from a source that, Sam has retired to Miami, much to his surprise. Jones and Diana do a bit of undercover work to find out which panel Anderson is interested in attending, so they can make the arrangements to trap him, accordingly. Peter and Neal talk about the origin of their relationship. Peter confesses that, he took the deal because he liked Neal. Peter then asks him about Sam, but Neal says nothing, as he seemingly is apprehensive about sharing any details regarding Sam, with him. The panel Anderson wants to attend will feature a one-of-a-kind prototype for a cutting edge bulletproof vest. If Anderson steals it, his company could make billions, therefore the team concludes that Anderson would put in all his efforts to steal the prototype. Mozzie on the other hand, sets up at the safe house where they'll wait for the person tracking Sam.
Neal says he's going to steal the tracking device when Anderson makes his move for the vest. Peter finds out much to his surprise that, the real Sam has been dead for three years. He and Diana as a result wonder who Neal has been dealing with all this while. Peter then tells Neal the news about Sam, and all that he has found out. Neal on his part isn't convinced, and tries defending Sam by telling Peter he's faked his own death several times, therefore his belief is that the Sam he is dealing with is the real thing. Peter though isn’t convinced, and instead thinks there's a chance the person claiming to be Sam is a corrupt cop, who is doing all that, he is doing because he has a vested interest. Diana tells Peter about the authorization for surveillance on Sam, so they can get to the bottom of things. Peter figures out that Neal is setting a trap and wants Diana to find Sam.
Later, the inventor of the vest meets with Peter. They tell him about Anderson, and what he is planning to do. His plan had been to demonstrate the capability by shooting a volunteer, but the conference wouldn't let him, as it’s a bit too risky. Neal on the other hand tells Mozzie about Sam possibly being a fraud and tells him, to stall the plan that they had put in place earlier. Just before the presentation Anderson slips Diana's tail. After the presentation they spot him in a stairwell planting plastic explosives, much to their shock and horror. Everyone is immediately evacuated in order to avoid a disaster and Neal based on the clues at hand realizes that, the inventor of the vest is the real target. There ends up being a shootout in the garage. Neal ends up saving the inventor, but gets shot in the process.
Fortunately he was wearing the vest, and therefore manages to escape unscathed. Mozzie tells Neal that Sam has "gone rogue". He didn't want to wait for Neal, telling Mozzie he was going to the safe house to handle things himself. Neal and Mozzie go to the safe house and find Sam being beaten mercilessly. They are able to rescue Sam. As they leave the house they run into Peter and send him back in. Peter loses him and calls for back-up. Sam doesn't have much in the way of answers for Neal about who attacked him, as he doesn’t seem to have an idea, but tells Neal the man doesn't know about Neal, from what he has summarized. Neal hands Peter a towel with blood from the man claiming to be Sam.
The idea is to basically conduct a DNA test, to find out if the Sam between their midst is the real deal. It is later discovered, based on the tattoo Neal spotted that, the man who attacked Sam is Dennis Flynn. His family was involved in organized crime in the DC/Baltimore area. This backs up what Ellen told Neal about his father's testimony. Peter is curious how Flynn had access to the FBI files. Peter and Neal return to the conference and finish their panel. It goes well, and there are no other disruptions.
Later, Diana tells Peter that the person claiming to be Sam is in fact not Sam, as she has found out from her investigations. Peter calls Neal while he's with "Sam". Peter then tells him something which isn’t heard. Neal is visibly surprised on hearing whatever is told to him. He hangs up the phone, and then turns back to Sam and says "Why didn't you tell me that you're my father?" with absolute surprise. The episode ends at this point.