The latest number that the machine dispenses belongs to Michael Cahill, who on the surface is an unassuming and upstanding but solitary citizen, which masks the fact of being involved in a major smuggling ring led by a man named Neil Vargas. Members of the ring will not hesitate to kill if anyone gets in their way. Reese quickly infiltrates the smuggling ring as one of their own. But when Reese follows Cahill away from the group, Reese finds that he is really Daniel Tully, husband, father and undercover cop, who is deep undercover. Tully could have long ago put Vargas away, but is waiting to nab the true ringleader, a man going by the code name L.O.S. Reese also learns that Vargas probably has a connection working inside the police force. While Finch gets Carter to provide information on the police workings of undercover cops, Reese gets Fusco to re-establish his connections with the dirty cops to flush out Vargas' connection inside. If anything goes wrong, it could mean the demise of Tully, Fusco or both. Seeing Tully's conflict of his work against wanting to be with his family, Reese remembers back four years earlier on his return to the US and wanting to at least know what was going on with his ex-girlfriend Jessica.
Reese discovers there's more to the story after he infiltrates a smuggling ring to get close to his latest POI.
- Finch gives Reese the latest name, a 33-year old Michael Cahill with no real family attachments. Cahill is a smuggler working for a dangerious guy named Neil Vargas (José Zúñiga). Reese poses as the driver for a job moving diamonds and we see that Cahill doesn't have any patience for mistakes.
Reese follows Cahill and watches him seemingly break into the home of a police officer named Tully. But inside he hugs a child (Skylar Gaertner) and kisses the mother, Melinda (Jill Paice). Tully (Michael Aronov) is working deep undercover as "Cahill."
Flashback to 2008: Reese, a CIA mission, has grabbed somebody Agent Snow (Michael Kelly) tells Reese is accused of selling software to the Chinese. While waiting for orders Reese is given some R&R in New York, where they are working.
In present day we learn that Tully has been undercover for nine years. Finch worries that someobody may have found out he's a cop. Tully meets with his Internal Affairs Bureau (Skipp Sudduth) handler who tells him they have enough on Vargas to pull him out of the operation. Tully says that the real target is "L.O.S." who is picking up the next shipment in person. This is apparently the "big one." He tells his handler that Vargas has a cop on the payroll.
Snow goes to see Carter and tells her they know Reese is working with a cop. He talks about Reese using people and makes reference to a past partner of Reese's. Finch shows up after Snow leaves and tells Carter that there is a leak that could jeopardize Tully's life. She tells him the handler is the only person who would know Tully is undercover. Files are kept in hard copy only and in one location, H.R., guarded by Internal Affairs.
Reese tells Fusco what's happening and asks him for some help.
At the next meeting Vargas gets a phone call that upsets him. He says he still wants to continue because if they don't finish the mission "L.O.S." will kill them. The deal goes south and Vargas' team opens fire. They end up leaving with the drugs but one of the guys, Ajax (Robin Lord Taylor), is shot and seriously wounded.
Afterwards Vargas has them make a pitstop and tells everyone to destroy their phones and give up their guns. Vargas then says "one of you is a cop" and vows to find out over the next few hours.
Back to the '08 flashback: Reese sits at a bar and strikes up a conversation with a man who turns out to be the husband of his ex-wife.
Finch calls Carter and tells her he's lost touch with Reese. He sends her a license plate number.
Using the wounded Ajax's cell phone Tully manages to send a text to his handler with his whereabouts.
Fusco asks about Vargas. Finch calls him with instructions to get into the H.R. room where Tully's records are held. He gets in and destroys the file. But Fusco is caught by Davidson (Reg E. Cathey), the head of H.R. who places him under arrest.
In the car Fusco starts to explain the situation. But Davidson gets a call from Vargas. He tells Vargas that a call was made from that location, then knocks Fusco unconscious.
Reese places the phone into his own pocket, taking the heat for Tully when Vargas dials the number. Reese is promptly hit over the back of the head. Reese is interrogated. Tully asks for time alone with Reese, who tells him he knows all about his story, including that the name of his wife and son, and that his brother OD'd. Reese says he can help him get home. Tully wants to stay under and try to bust "L.O.S." Vargas returns and wants to kill Reese. Tully says he wants to do it and shoots Reese in the shoulder.
Back in '08 Reese's partner, Cara Stanton (Annie Parisse), wants to know why he's snooping around Peter, the new hubby of his ex. She tells him that Peter could take better care of his ex than he could and should leave them alone. Peter wants to introduce Reese to his wife, since they're from the same town. Reese's partner convinces Reese to leave.
Reese and the more seriously wounded Ajax are placed in the trunk of a car, which is set on fire. Tully manages to slip Reese a flashlight that helps him escape at the last moment. Carter arrives and Reese tells her that Tully only grazed him. Finch calls and Reese tells him Tully is headed for the pick-up in Brooklyn. Finch tells him about Fusco and says he's not sure if they have time to save them both.
At the meet Tully grabs "L.O.S." (Michael Berresse) and puts a gun to his head. Vargas points a gun at Tully, but Reese and Carter arrive in the nick of time to gun down Vargas and the rest of the "L.O.S." team. Reese knocks "L.O.S." out and tells Tully that the guy is CIA and taking him in will only jeopardize his career. Tully says he's doing it anyway.
Davidson places Fusco on the ground and is about to kill him. "You think you're the first person to put a gun to my head?" Fusco says without turning a hair. Davidson responds, "No, but I will be the last."
At the last second Reese shows up and shoots Davidson, saving Fusco's life. But Reese destroys the dead cop's phone and tells Fusco they need him to remain dirty. Fusco is "more useful inside."
Finch and Reese, watching from a car as Tully takes his wife to the hospital to have their second baby, discuss the fact "L.O.S." is about to be released.
Snow picks up "L.O.S." at the station. "L.O.S." wants Carter and Tully taken out, but instead Snow has "L.O.S." killed right there inside a CIA SUV.
Fusco buries Davidson and gets help from another dirty cop Simmons (Robert John Burke). He tells Fusco that he "belongs to H.R. now."