[Season Finale – Part 2] In voiceover Michael Westen said that "in a crisis the mistake was to act too soon, before you had assessed the threat." Sam told them that “It’s really bad.” Any time he called even the Carlito there was a major response at FBI headquarters from something that Vaughn was telling them. They needed to come up with something and Sam had the idea of who to “make friends with” and take the thumb-drive to: Bill Cowley. Back to her old obstreperous self, stashed in an out-of-the-way motel, Madeline whined about being asked to approach Bill Cowley again saying “it amazes me what becomes ‘normal’ to you guys.” She threw a sign at Sam’s head and howled “you put me in a non-smoking room” before she lit up. Vaughn called Ms cell phone number and they found that Vaughn had routed it through 3 different numbers when they tried to trace it. He said he was "tired with this coy crap. I gave you a chance to be friends so now you are going to see what it’s like having me for an enemy… and so are your friends and your family." M decided to smuggle the thumb drive into a nuclear facility for safe keeping – somewhere that even if Vaughn found out where it was, he couldn’t go get it.
Incredibly, as Fiona was planting her last C4 she did her usual whining about “what this means for us” one to many times; M told her that “maybe this isn’t your path” which shut her up for about the two seconds it took for Jesse to rush in saying that Vaughn’s men were there talking to the guards at the gate! They sped away with the obligatory black cars racing after them, only this time hanging out the windows shooting machine guns! M hung back to block bullets then decided to phone Fiona to pull up alongside. He jumped out the window of his car and into Fiona’s car leaving her explosives to demolish the charger and block the road. Yet another car chased them into a crash at an abandoned hotel with a rebar sticking out of Jesse’s leg. The siege began. Their cell phones being blocked, Fiona escalated her self-centered accusations and whining while doing first aid on Jesse. Vaughn called on the hotel phone and M told him if he wanted the thumb-drive he had to come and get it. Fiona and Jesse set up some explodables they found in the hotel while M went to the roof to trigger the weather device into telegraphing a hurricane and nuclear attack. Waiting for Vaughn to breech, Fiona whined to Jesse that she was expecting M to do the burn notice thing and get it out of his system. Even Jesse asked her how she could figure she would change M to her own specifications.
Madeline got into Cowley's fund raising dinner and got him to come out to talk to Sam by saying he’d won his last election by 76% of the vote so they must be good people to talk to. Of course he didn’t believe anything Sam said, but was intrigued when Sam told him confidential information about Barrett’s metal case containing the list. Fiona waited until Vaughn’s men got inside then shot the propane canisters to explode on them. When he got to the roof, M had to take down a SWAT commando in order to set off the weather transmitter; but then did get his vest and weapon. However, a sniper on the roof of an adjacent building began shooting at him and he had to devise an emergency rappel in order to escape. He tied a rope to an anchor – the other commando – and jumped off the building dragging the guy across the roof until he stopped with a jerk. They watched as several cop cars came in response to Ms emergency signal but they were turned back by one of Vaughn’s men. Vaughn called to gloat saying that one of the men on his NOC list was in Homeland Security and had told them that they were in a training exercise. Just like Marv’s case of arrogance, Cowley said "I know what I’m doing" when Sam warned him about going only to the top because "they" would find out if he used the chain of command. Sam sent Madeline back to the motel and waited for Cowley to come around. Cowley was just telling him that he would not help when he was advised that his request for an FBI background check had just triggered an APB on him for ‘protective custody’ reasons. He then finally decided to escape with Sam.
M and Fiona were using fertilizer from a gardener’s closet to booby-trap a stairwell and Jesse prepared the elevator shaft for them to escape down. Fiona called Vaughn to make a deal and ragged on M yet again to “say something to Jesse” before this ends. M told her to focus on saving his life for now. Sam had Cowley call back his higher level contacts to help them get around the cops who were trying to capture them. Vaughn called Fiona to say he was ready to come up but just for security reasons he had captured Madeline on her way south and was bringing her with him. Madeline told Vaughn to “go to hell you bastard.” One of his guys hit her in the head and bloodied her. Given the phone to assure M she was alright, she instead blurted out that they had shot her and it was a trap and to run. M told then capitulated and told Vaughn that he was coming down. His plan was to get to a shack with an explosive and when Vaughn's men came he would set it off in order to give Fiona and Jesse enough time to get out with the list. M gave Jesse the thumb drive and said he was "truly sorry" for what he did to him. Jesse, after all this, decided that he really didn’t need an apology. Fiona still looked distressed so M told her that maybe she was right this isn’t your fight.
M took a run for the shed through sniper bullets coming from all directions and eventually crashed through the shed's window. Vaughn told Madeline to get in his car in the window seat so she “could watch me kill your boy.” She responded by spitting on him. Halfway out of the building Fiona kissed Jesse and said her place was back with M. So she ran the gauntlet too and joined M in the shack. They decided that they would push the switch to the bomb together. As Vaughn stumbled his fat butt out to advance on the shed, flash grenades fell and a band of military stormed in. When Vaughn screamed they had no authority here he was cold-cocked by a haymaker from Sam who said, “say another word I dare you.” As Vaughn was hauled off in handcuffs Madeline told M that she was alright and to go see his friends. Sam said the troops came from Cowley and Jesse passed the thumb-drive back to M in a handshake. Two guys in suits, without sunglasses and saying they were not with the police, approached M and asked him to come with them so they could ask him some questions. He kissed Fiona goodbye; but didn’t say anything to Madeline.
Next we saw of M he was groggy in the back seat of a limo with two government types, after having been interrogated for a week. They stopped the car and handed him a trench coat saying to get out. It turned out that he was in Washington DC, in the snow, in front of a government building – we know because when the camera pulled back we saw the capitol in the background. A friendly looking guy came out of the building, smiling and Michael simply greeted him with “you!” “You” held out his hand and said: “welcome back." M tentatively took it then “you” nodded his head in the direction of the building implying that M had the choice to come in or not – he did.