The episode opened with things looking bleak. Control (Camryn Manheim) and Hersh (Boris McGiver) had the upper hand, with Harold Finch (Michael Emerson), Arthur Claypool (Saul Rubinek) and Samantha Shaw (Sarah Shahi) all under the barrels of guns in a supposed safe room. Shaw was just about to be taken out with two shots when Root (Amy Acker) burst in, wielding dual pistols. After a frantic shoot-out, Hersh wound up shooting Root from behind while Shaw, Finch and Arthur got away. So did Control and Hersh, with Root in their custody.
Finch and Claypool, who was dying from a brain tumor, found a bank deposit box that was supposed to hold the code for Samaritan, Claypool's creation that was similar to the Machine that Finch had created. Problem was, the privacy zealots Vigilance also joined the party and took over the bank while Finch and Claypool were in the vaults below with the bank manager. Finch locked the vault door to keep Vigilance out, but not before the manager got wounded in the leg in a shootout. To make matters worse, Hersh was one of the people leading the SWAT team outside the bank. (I would not have taken the odds on Vigilance were I were a betting man.) Shaw was still hiding in the bank lobby, communicating with Finch.
On the other side of the country, John Reese (Jim Caviezel) and Lionel Fusco (Kevin Chapman) were in a holding cell, hashing out the meaning of what they were doing. Fusco said he wanted to keep fighting the good fight while Reese saw it as pointless. Fusco gave up in disgust and signaled that he was ready to leave. He did mention that he hadn't heard from Finch and suggested that he might need their help.
After some time, Vigilance ran out of patience and decided to blow the vault, but Shaw rigged another bomb nearby so that an escape route through the sewers would be available. Claypool smashed the code for Samaritan under his foot. They were nearly ready to leave when Vigilance caught up, only to have Fusco and Reese appear to save them. Hersh had some Vigilance pinned down as well, but one of them was holding a grenade and detonated it. Chances are very high that Hersh survived, though, since he could probably live through a nuclear bomb.
Root's situation played out thusly: She was held in a cage by Control and was alternately being given barbituates and uppers to get her to talk. Root kept begging the Machine to help, which caused Control to smirk and keep asking her to tell her where the Machine was. Root scoffed and said that the Machine was too complicated for the likes of her Finally, Control cut an important bone out of Root's head - one that controlled sound from the ear to the brain. But it turned out the Machine had been talking... at a level of sound that Control. who was in her 50s, could not hear but that the younger Root could. It gave her important information, like where Control kept an extra scalpel on her body, an area that Root could reach when Control was performing her 'surgery.' Root freed herself and took control (snort) of Control. She talked to the Machine and it told her to tell Control to leave it alone, telling Control that it was watching her at all times.
Finch sat with Claypool, who was back in a hospital bed, waiting to die. He told Finch that he was losing memories. Finch said that they weren't destroyed and then Root called and told Finch that finding the Samaritan code was her problem. She then had the machine play back memories, happy ones, for Claypool to watch before he passed on.
Reese, who had just rescued Finch, said that he couldn't stay. He felt the Machine had let him down when Joss Carter died and that it didn't really care who lived and died. He left while a bereft Finch could only watch.
Apparently the bank manager had actually been a plant - the real manager was killed just before the three had entered. Unfortunately, that loose end was tied up by the mysterious man who has Finch in his sights. He shot the woman and he now had the Samaritan Code.
The episode also showed flashbacks to Finch's life, including his talking to his increasingly dementia-addled father about machines and his hacking the government. It also showed the genesis of the Harold Finch name: He pressed a bird-watching book into his father's hand as he was fleeing being questioned about the hacking. Hopefully this will end up in something really good.