The episode opened with Sameen Shaw (Sarah Shahi) asking Harold Finch (Michael Emerson) where John Reese (Jim Caviezel) was. Finch said Reese would return when he was ready. Finch then ignored the Machine trying to give him numbers. It turned out Reese was at a bar in Colorado. Clearly still hurting from Joss Carter's (Taraji P. Henson) death, he walked away from saving someone who was being beat up and also he started drinking heavily.
Back in New York at the Library, Root (Amy Acker) was somehow communicating with the Machine too and told him that he was still needed and that he shouldn't ignore Her, meaning the Machine. He decided to help out and recruited Shaw to take over in Reese's absence. She was sent to play doctor at a local hospital, since the Number was a guy with a terminal tumor: Arthur Claypool (Saul Rubinek). Finch seemed stunned at first when he saw Claypool's face on his computer monitor. The tumor was affecting Claypool's memory and he was saying things that shouldn't be leaked, possible state secrets, and he had a Secret Service detail monitoring him.
There were a series of flashbacks throughout the episode, spanning a decade from 1969-79, with a young Finch and his increasingly-forgetful father who was suffering from what seemed like Alzheimer's. The phrase "If they want to keep me out, they need to build it better" was said often. It was interesting to see, though the flashbacks didn't illuminate much else about the character of Finch except to show how incredibly smart he was, which we all know anyways.
Claypool's wife, Diane (Camryn Manheim) came to the hospital. After an unsettling scene where he kept saying he didn't remember Diane, Shaw talked Diane in the coffee room. It turned out Claypool never talked to her about his work. She was broken up over how he had changed. After the conversation, Shaw found Claypool out of his room. It turned out he was in radiology. Finch chirped in and told her that he was in the NSA, which meant he was likely shouting secrets that many Bad People would love to get their hands on. Seeing a security detail outside the radiology room, Shaw got in there via a more unconventional way, through a ceiling tile. She found a syringe with sodium pentothal: Claypool wasn't be examined, he was being interrogated. She saw the would-be interrogtor -- a woman -- leave the control room and then of course, the Secret Service burst in. Side note: Shahi was doing really good job playing the "Reese" role with Finch during this whole thing.
Shaw was locked in a hospital office. A cell phone in a desk rang. It was Finch, who had driven to outside the hospital. He was reluctant to come inside, electing instead to try to figure out who was trying to interrogate Claypoool: it turned out to be a woman named named Elizabeth Ross. The agent began trying to question Shaw, who gave him a very hostile glare.
They cut to Reese at the bar. He walked past a table with a guy reading the paper. He yanked off the cap the guy was wearing: it was Lionel Fusco (Kevin Chapman). Reese kept him at arms length, but Fusco was not going anywhere.
Back at the hospital, the Secret Service agent interrogating Shaw got flushed and collapsed. His food was spiked. Shaw extricated herself and got to Clayman's room to try to get him and Diane to leave. There were people coming into the hospital: it was the Vigilance group I mentioned before. Things were going badly, Clayman was refusing to listen to Shaw, but then Finch came into the room. Clayman recognized him. Now mollified, Shaw and Finch got him out of his hospital bed, with Claypool reminiscing as they were walking along. Apparently the two went to M.I.T.. There was a brief shootout between Shaw and the Vigilance people, but Team Finch was able to get Claypool and Diane out.
At a hotel, Finch was asking Claypool about the things that Vigilance was asking about in the radiology room - about someone named Rudy and a program called 'Samaritan'. It turned out -- get ready to have your minds blown here -- Claypool had made ANOTHER Machine. It could remember and learn and was a real AI. I'll wait while you process that. Claypool said that Samaritan was destroyed in the wake of 9/11 and also because someone had already built a machine (Finch tried to keep a poker face at that but seemed to fail miserably).
At the bar, Reese chided Fusco for not drinking, only to have him retort that he was two years sober. It was because of Reese and then he got on him for his self-pity, saying that he wasn't the only one hurting. Reese said that that it was all pointless, which set Fusco off, since that pretty much intimated that the cop was pointless. Fusco decked Reese through the door outside and they fought, though Fusco lucked out, what with Reese having his reflexes dulled slightly by the drink. After a fight that was coordinated as well as a WWE match, police sirens broke it up. Carter would have probably smacked both of them for fighting.
At the hotel, Claypool was arguing with Diane again, and Finch tried to reassure his friend that it was his memory playing tricks on him again due to the tumor. That's when Claypool said something chilling: "No. I remember my wife. I buried her two years ago." "Diane", realizing that that the ruse was up, spoke into her watch and a bunch of agents burst in, subduing Shaw at gunpoint after a bit of a fight. Then even more of a shock: The assassin, Hersh (Boris MacGiver) entered. To make matters even worse, it turned out that "Diane" was really Ma'am from Control, Shaw's previous employer. She said that only one person between Claypool and Finch would leave alive. It cut to the Machine calculating survival percentages (Shaw had nearly an 85% chance of dying - yikes). Then ... from somewhere ... Samaritan seemed to be activated again.
The next episode is going to be on Jan. 7, which should be enough time for people to re-assemble their brains after all this. See you all in 2014.