Reese and Finch team up with surprising allies in a race to save The Machine from Root and the mysterious international organization Decima, who have both re-emerged with dangerous agendas. As the POI team faces off against enemies old and new, the nature of Finch's relationship with former partner Nathan Ingram is revealed along with his original motivation for wanting to save The Machine's irrelevant numbers. Meanwhile, in her mission to bring Cal Beecher's murderer to justice, Detective Carter finds herself up against the criminal organization known as HR.
By the end of the episode, four entities have an interest in the Machine: 1) Finch, Reese and their new-found ally Shaw; 2) Special Counsel and the Project; 3) Root and; 4) Greer and Decima Technologies.
NLP (Natural Language Processing): The capacity of a computer to understand spoken or other forms of natural human language, that is, a computer's ability to understand spoken or written input.
In this application, it refers to the Machine's ability to understand input such as the text embedded in the blue screen codes or Finch's spoken commands.
HMT (Hybrid Machine Translation): The system by which a computer can translate one natural language (e.g. English) to another (e.g. Spanish) using a combination of machine translation paradigms. In the scene pictured, the Machine analyzes the shooters' Macedonian dialogue (NLP) and translates it into English for the audience (HMT).
Nuclear Reprocessing: Extraction of residual uranium and plutonium from spent fuel rods, used in nuclear power plants, in order for it to be reused for other purposes.
According to the DVD commentary, the scenes with Enrico Colantoni (Elias) and Carrie Preston (Grace) were filmed at different times than that of the bulk of the episode. Preston's scenes for this episode and Zero Day were filmed several months earlier, before she returned to Los Angeles to begin work on the current season of "True Blood." The close-ups of Colantoni were filmed in front of a green screen after main production was completed; a body double was used for the longer distance shots of Elias from behind and with the bag over his head. Colantoni was in Portland filming a pilot during main production.
On the commentary, Jonathan Nolan frequently describes what the production refers to as "MPOV" or Machine Point of View, the scenes we see from the Machine's perspective.
In a blog post, producer Jonathan Nolan notes that his only regret about the final version of the episode was that there was insufficient time to show "delicious" flashbacks of how the Machine moved itself.
The working title for this episode was "Flashbacks". 
When Finch follows Nathan to the ferry, he isn't carrying a bag of any kind, nor is he seen to be carrying a book. When Grace looks at the personal effects recovered from the scene of the terrorist attack, however, she finds the book into which Finch placed her engagement ring when he proposed to her. ("Zero Day")
When Shaw shows Reese the boarding pass she took from Lawrence Szilard's briefcase she says that the airport in Portland is the closest airport to the Hanford Site . In actuality, Seattle-Tacoma is almost an hour closer.
Reese and Shaw are seen driving a facelifted Mercedes Benz W221 S-Class during the police pursuit scene, however after they exited the expressway by literally crashing off the side they were seen emerging from an older model Mercedes Benz - the previous generation W220 pre-facelift. The headlights of the overturned vehicle are a clear indication.
When Reese and Shaw steal the car, the Mercedes Benz 3-pointed star is correctly mounted on the hood. In the next scene, it is missing.
When Finch comes into view with crutches at the beginning of the episode, asking the Machine, "Did you know?" the narrative is constructed using in medias res (medias: middle), a non-linear storytelling technique where the narrative starts in the middle of events and uses flashbacks to bring the reader up to the point of current.
According to the episode commentary on the season 2 DVD, in addition ot the cameo by Plageman, Nolan and Lewis, this episode also features cameos by producer Richard Slack (as the Kidnapped Man), writer's assistant Brigitte Liebowitz (the first picture removed from the safe in Finch's office), writer/producer Amanda Segel (a woman walking into a building, from MPOV), and assistant director Michael Pitt (the groom threatened by the Jilted Man). The scene with Amanda Siegal was filmed in Los Angeles, where the writers are based.
Both the first and last episodes of the season begin with a flashback of Finch talking directly to the Machine. According to Nolan, this was originally planned for the pilot, but cut from an early version of the script.
Root was introduced as a psychiatrist in Firewall, under the alias Caroline Turing. In God Mode, we can see the irony of her being incarcerated in a psychiatric facility.
The day counter used in the flashback changes from 4138 (the days since the machine was activated) to day 1 after the hard reset.
In the pilot, the floor in the room containing the machine has white tiles. The presumably raised floor (often used in server rooms) is seem to be removed as well because in this episode the floor is all grey.