Danger closes in when the battle to bring the crime organization HR to justice reaches new heights. Also, when the Machine suddenly gives out Reese’s number, the POI team faces their greatest threat yet.
The publicity campaign for the episode arc which includes this episode was designed to lead viewers to believe Lionel Fusco was going to die in this episode. To help keep the secret, an alternate ending was filmed in which Fusco catches the bullet. Creator Jonathan Nolan referred to their efforts as "the big lie."
When Carter tells Finch that she has deduced that he is using a computer receiving government feeds to identify the people who need help, he confirms it and the Machine acknowledges her deduction by assigning her a yellow box.
Root mentions to Finch that John was not his first "helper monkey". Later in the season, “RAM” introduces Rick Dillinger, an operative whom Finch recruited prior to hiring Reese.
Finch mentions the axiom, "divide and conquer", which refers to a military strategy where one side attempts to divide the opposing force into smaller units that can then be more easily defeated in battle. In common usage, it has become an expression for the process of breaking up any large problem into smaller, manageable units, or to separate allied people in order to win an argument. In computer programming, divide and conquer is a widely taught method of breaking a programming problem into manageable computing tasks.
At the precinct, Reese and Carter replay some of their dialog from when they first met. Later, Carter dies at the same spot where Finch's private security picked up Reese in the pilot.
After the shooting we see Reese and Carter on the ground through a camera but neither one has a box. This may be an indication that even the Machine has reacted to Carter's death.
The length of Fusco's tie changes after he leaves Lee's room and closes the door.
When Finch meets Carter at the 8th Precinct, the station's sign is missing.
At the end of the episode, when Finch is talking to Carter, he refers to Reese as John Doe, however it's clear this line was dubbed as his lips say some other name.
One scene takes place is a station signed as "Queens Plaza". However, the station shown is a two-track single platform design, while the real Queens Plaza has a four-track double platform configuration. Also, Reese, Carter, and Quinn exit a 7 train in a subterranean station; the 7 stops in the elevated Queensboro Plaza station located above Queens Plaza.