How does Fusco know who he can safely call for backup when Elias is breaking into the safe-house? Thanks to his work as Reese's inside man in HR, he knows just about everyone who isn't an honest cop in New York, and called somebody who wasn't on that list.
Extremely subtle but Finch becomes panicked when someone he cares about like a POI or John is around a bomb. Later in "God Mode", we discover why Harold's Only Friend Nathan Ingham was killed by a bomb while Finch had his back ruined in the blast. After this trauma, when someone he cares about is around one, Harold immediately drops everything and if possible is willing to die trying to save them from getting blown up like in the case of John during "Dead Reckoning"
John Reese was likely the first number from the Irrelevant list that Finch was able to save. (His number came up prior to the events in New Rochelle, and then he was contemplating suicide when we meet him in the Pilot episode 7 months later.)
Reese pronounces the Dutch commands he uses with Bear with a heavy German accent. If he was stationed in Germany during his military career, he might have picked up the language there. Then he ends up in Iraq, where he starts working with dogs trained to respond to Dutch commands—and his pronunciation of the Dutch words is colored by his prior experience with German.
The Machine was infected by a virus sent by Decima, but inside that virus was another virus which caused it to protect itself from all attempts to gain control over it. Finch didn't make a virus: he made a vaccine.
Why does Root open fire in the asylum three seconds before Hersh steps into the corridor? The Machine is giving her the ability to detect the position of hostiles which was displayed in "God Mode", as a result, she's able to basically lay down suppressing fire and force Hersh to dive into cover, catching him off guard.
Lionel Fusco's days with Stills and the nascent HR hierarchy gave him the skills needed to figure out how to "mock up" crime scenes to look the way a cop wants it to look, so when Carter needs a faked death, Fusco already has everything needed.
"Endgame" reveals how Carter immediately knew Reese had suffered from PTSD back in the "Pilot" episode. Her husband who was a fellow veteran displayed similar traits as their marriage fell apart.
Root's alias Caroline Turing in "Firewall" probably refers to Alan Turing, Father of Computer Science and Artificial Intelligence.
When Reese is tailing Benton near the beginning of "Cura Te Ipsum", Benton carries a woman's briefcase as they walk to work; this same woman is the lady who recounts being raped by an unnamed co-worker at the survivor meeting, and her photo also shows up in the files that Reese downloaded from Benton's computer. The worst part about this is that although we don't know when he raped her, it happened sometime before the events in the episode and so she has to face the man who raped her at work every day. Not only that, but judging from the fact that he offered to carry her briefcase he makes sure that she has to see him.
Finch was on the phone with Donnelly when Stanton crashed into his SUV with a dump truck. He would have heard the crash, but have no idea what happened. Imagine how terrifying that would be.
Is it just me, or was the scene where the fake Agent Fahey is about to kill Finch really creepy in an understated way? He has an almost childlike sense of glee as he says, "Are you... like me?" and then he takes Finch's glasses (in a very real sense, stealing an iconic piece of Finch's identity) and puts them on as he begins telling Finch he will become the new "Finch".
Subsidiary: Imagining an identity thiefnote the "serial killer" part is just a bonus, considering that the "irrelevant" numbers are people who would either be dead anyway or would be thrown in jail. Either is convenient from the perspective of "Fahey" in this episode. being in control of The Machine is too horrible to contemplate.
OTOH, the real horror would likely be for "Fahey", as he has no idea what he would be getting into and how many enemies he just acquired.
Also, he wouldn't be in control of the Machine. The Machine knows who 'Admin' really is, and anybody else claiming to be would be summarily ignored.
Equally creepy is "Fahey" repeating his words over and over to pick up Finch's intonation and really become him.
The fate of Hannah Frey. She was kidnapped and murdered. But you have to wonder exactly why. If he was just a sick killer, or if it was for perverse reasons... Definitely not helped by the fact that he redid the porch two weeks after she disappeared.