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The show opens up with Root's voice cutting off Finch. For the first time, we’re given a look on Root's side of the operation.
Root helps a man named Billy escape a prison bus. She takes him to complete a few tasks in order to intercept a package, all while taking orders from the machine from the chip in her head.
She leaves Billy, and the police show up to take him back to prison. She enters a building, waiting for the computer to give her further instructions. It directs her to a janitor named Cyrus.
Finch catches up with Root while taking a walk with the Janitor. He explains to her that the moment she approached Cyrus, the computer gave Finch his number. He believes Root is putting him in danger, but she believes she is protecting him.
Root and Finch speak about the Samaritan, a machine that will destroy the computer that gives them information that saves people’s lives.
Finch tells Root that Cyrus was very educated and was once rich, but now works as a janitor. Root leaves with Cyrus, and sends Finch a picture message about a male enhancement pill.
Shaw and Reese show up, and Finch tells them to trail Root while he tries to decipher the message. Reese makes a joke that maybe Root wants to hook up with Finch.
Root and Cyrus are at his home, and she is trying to get him to pack up since he is in danger.
While going through his stuff, she finds a picture with two other people in it with Cyrus, but he won’t tell her who they are.
Just then, a sniper tries to take out Cyrus, but fails. Shaw sees the sniper and heads in their direction while avoiding being shot at by a group of men who also showed up. She loses her cell phone, and therefore cannot connect with Reese and Finch.
Finch discovers that the picture contains a hidden message and tries to unveil its contents.
Root and Cyrus escape out the window, while Shaw reaches the sniper, and Reese takes care of the men who found their way into Cyrus’ apartment.
Finch finds out that a group named Decima Technologies is after Cyrus, as well as some unknown organization.
Root gets Cyrus arrested to protect him from being taken or killed.
Shaw, without any way of contacting Finch, is trapped in the building where the sniper, who was later killed, was hiding. A man tries to get Shaw to join their team of vigilantes against the government that betrayed them.
Fusco clears Cyrus’ charges and prepares to bring him to Finch, but Root shows up with a warrant to take Cyrus instead.
Root calls Reese on a pay phone. Reese tries to convince her to hand over Cyrus, but she refuses and hangs up.
Root questions Cyrus again about the picture she found. He reveals that the two people in the picture, Sara and Alex, were his best friends from college who started a finance firm. The small firm became bigger after the stock crashed, and their firm grew as a result. One day, someone came in shooting and killed them, injuring Cyrus.
After the incident, Cyrus gave all of his money to charity, and works as a janitor at the firm’s old building, keeping the place clean.
They leave the diner, but are suddenly cornered, and Cyrus is taken, with Root's implanted chip being damaged in the process.
The team figures out that Cyrus’ eye can access a retinal scanner for a door that protects a computer chip. Decima plans to use Cyrus to steal the chip to help enhance the Samaritan system.
Root forces Finch to fix the chip so she can put it back in her ear and connect with the machine again.
Root reveals that she was paid $15 million to kill people at a financing firm, which turned out to be the firm where Cyrus worked.
After a long talk about humanity and doing the right thing, Root takes the device Finch was working on and leaves. We see that she leaves behind a piece.
She goes to a doctor and forces him to fix the chip implanted in her head
Meanwhile, Cyrus is forced to unlock the door to the chip. Once the men are let in, the boss orders them to kill Cyrus.
The men are about to kill Cyrus, but Reese and Fusco show up and get involved in a shooting match.
Root shows up, and is standing at the door to the lab containing the chip. Instead of going inside, she hears the gunshots from Reese and Fusco, and goes to save them instead.
She manages to save Cyrus and gets shot in the shoulder as a result.
By the time Reese reaches the lab, the men are already gone with the chip.
Back at home base, Shaw shows up, wounded from fighting her way out of the building.
Cyrus leaves to try and live a better life, and the machine sends Root to her next destination. Finch asks Root to work together since the machine that Decima is building could destroy theirs, and there is a silent understanding between them. Fusco arrives to bring Root to her plane, and she is gone, but will show up again.
The episode ends with a status bar that shows Decima uploading the chip’s contents into their Samaritan machine.