The show does not hold the federal government's institutions like the FBI and CIA in high regard. To be fair, this is par for the course in any crime/espionage drama, and both organizations do/did have some good people in there (such as Agent Donnelly, Detective Carter and John Reese) and it's clear that the show is a fan of showing how many corrupt people are in law enforcement agencies in general.
Banks in this show are almost always shown foreclosing someone's home, involved in illegal activity (willingly or otherwise) or shown to be incompetent. "Mission Creep" even features a confrontation in which a pair of bankers harass Reese and an ex-soldier in a bar.
Anvilicious: The show holds war vets in very high regard, and as stated above, frequently holds big corporate guys in very low regard. However, two notable early exceptions exist: "Mission Creep", where a group of active duty American soldiers are the bad guys, and "Risk", in which the stock trader POI is sympathetic and entirely in the dark regarding the dirty dealings of others at the office where he works.
Ass Pull: The ICE-9 virus is an example of a poor execution of Chekhov's Gun. It is introduced out of the blue in the third-to-last episode with the sole purpose of destroying Samaritan two episodes later, and much of the uncertainty surrounding it is in regards to the fact that it will destroy The Machine as well.
Just going by the forums at Television Without Pity Detective Carter or her actress, Taraji P. Henson, were this in the first season. Inverted as of the Season 3 "Endgame" three-parter, with Carter now being considered one of the most popular and beloved characters and her death leading to a violent online backlash and much tension between those that despised the move to kill her off and those that accepted the decision or the way that her death played out as she successfully rended the big bad HR useless and after what she did, even if they tried to rebuild, they could never be as strong as they were and have as much influence as they had.
Iris Campbell and her relationship with Reese. Many people found the ethics of the situation highly questionable (as Iris did in-universe) and didn't like the overtly romantic subplot or how quick it developed. A big part of the problem is that the whole thing was cooked up very sloppily after a bit of Real Life Writes the Plot ended the plan to kill Reese halfway through the season and they suddenly needed to give him something to do. She's then very off-handedly Put on a Bus in Season 5, making clear that no one on the crew really cared for it either.
The final moments of "The Crossing" divided the fanbase.
As of the end of season 4, there's an argument over the change of structure of the show, specifically with how POI is changing into a more "serialized" and complex format while discarding the "case of the week" episodes. Detractors believe it's making the show to hard to follow while supporters claim it makes the show a whole lot more interesting. A big complication is that the latter was always the kind of show Nolan and co. wanted to make, and the more episodic style was simply the only way they could get it sold to a network in the first place.
The fact that Finch had a happy ending. While more than a few fans were satisfied that Finch was able to live with the love of his life, there were others that would disagree. Some feel that Harold was a both a Failure Hero / Small Steps Hero until the later parts of the series which had enabled Samaritan to kill so many people in Season 4 and 5 (including, and especially, Root and John). They felt it was massively unfair that he got the Happy Ending that his inaction had denied to those victims their own happy endings.
The Genre Shift from a Post-Cyberpunk science fiction procedural to a Post-Cyberpunk science fiction caper show with Spy Drama elements. Some fans love POI for evolving. Some would have preferred to keep the human-scale stories of the original premise.
Complete Monster: Alex Declan, from season 2's "Proteus", kills his victims and steals their identities. After recently murdering Special Agent Alan Fahey, his eighth victim, he steals his identity as well and later assists Finch and Reese in trying to uncover the killer on Owen Island to divert any suspicion from himself. During the investigation, Declan murders the island's deputy, framing a Marine in the process and endangering several civilians. When Finch discovers that Declan is the imposter, Declan takes Finch hostage and attempts to murder him so he can steal his identity like he did his other victims. Although Declan believes the identities he stole were being "wasted" and that he "did them justice", Finch ultimately deduces that he kills people because he enjoys it.
Crazy Awesome: Root. Evident when she's in a shootout with Hersh, a trained assassin and shoots him when she has her back to him.
There were similar complaints about Sameen Shaw in Season 3.
Darkness-Induced Audience Apathy: It can be hard to get into the show and grow to care for anyone if you started watching it late, knowing how everything goes to hell in Season 4, how Decima is fast approaching Villain Sue status, and how Bear is the only character the writers explicitly said they would not kill off.
Dear Negative Reader: The show runners have been forced to utilize this trope after "The Crossing" aired.
Fanfic Fuel: The reveal that the Machine is running other teams across the US in addition to its main one.
Fridge Brilliance: Throughout the first three seasons, Finch's attitude towards the Machine is cautious and wary. It only becomes more pronounced when the Machine starts acting outside of its original parameters, even though it seems to be benevolent. This is explained in "Prophets", when we learn that Finch's first 42 attempts at creating the Machine all began self-improving at an exponential rate, and attempted to escape from the IFT servers or even kill him outright. That's the reason he implemented the memory wipe, and now that the limitations he put in place are gone, he's afraid that it will go rampant like its predecessors did.
Root's handle. Having root access on Linux is the same as being an administrator on Windows: you can do pretty much whatever you want to the system and it won't try to stop you. This could be a double bonus, seeing as the Machine thinks of Finch as 'Admin', indicating that she's his equal in hacking skills.
Her aliases are all connected to famous, innovative and eccentric scientists: Turing, Dyson, Neumann.
In one episode Finch is reading It Can't Happen Here, the 1935 novel by Sinclair Lewis about a dictator who takes over the United States. An interesting choice for someone who designed the ultimate Big Brother surveillance system.
When translated back into English, the blue screen codes that appear in the later half of season 2 are revealed to be excerpts from various books and published documents.
The title of Episode 17 of Season 2: "Proteus" has two meanings. Proteus is an early sea god in Greek Mythology, which makes sense considering the setting. The word "protean" derives itself from the god's name, which means "versatile" and "capable of assuming many forms". That's especially fitting for an episode about an identity-stealing serial killer.
"The Devil's Share" is the psychological term which refers to that part of human behaviour that allows us to be cruel to one another, or refers to one person's inhumanity to another. It also refers to an individual's actions that are not good for him/herself or for others, highly appropriate considering John Reese goes on a highly self destructive roaring rampage of revenge regardless of his gunshot wound and innocent people that get in his way due to Carter's demise in "The Crossing".
"Lethe" and "Aletheia", Greek antonyms meaning "forgetfulness" and "truth". Given the condition of the number for those episodes, very apt.
Also from "Aletheia," the Morse code that the Machine is using to communicate with Root (which, as she says, really can't be heard by anyone over forty because it's too high-pitched) is accurate and can be translated to confirm some of the things Root is saying.
SORRY. INCREASED PERSPIRATION. HEART RATE AND BREATHING ELEVATED. INDICATIVE OF FEAR. 2 OCLOCK. 2007 ANTERIOR CRUCIATE LIGAMENT TORN. SURGICAL REPAIR PARTIAL SUCCESS. 2010 PHYSICAL THERAPY DISCONTINUED AGAINST DOCTORS ADVICE.
"Deus Ex Machina"; translating as "god from the machine"...It also refers to the situation which Harold finds himself in at the climax. Alone and with no one seemingly coming to save him from Lambert aiming a Glock 19 at him, Reese barely manages to get up there in time and screw up Lambert's aim.
Greer quotes Hamlets famous What a piece of work is man speech to defend his worldview. Any true Shakespeare fan knows that speech is actually meant to be said with bitter sarcasm as Hamlet condemns humanity, showing just how misguided Greer is.
Harsher in Hindsight: In the show, the Machine produces the relevant and irrelevant lists by monitoring NSA feeds and other forms of electronic information gathering. Then came the real life June 2013 reveal of the US government's PRISM program. It takes a turn for Hilarious in Hindsight once you remember that Finch black boxed the Machine precisely because he didn't trust the Powers That Be with unfettered access to the Machine and the information it handles.
The next-episode promo after "If-Then-Else" suggested that Shaw might still be alive, pretty much ensuring that this reaction would happen. As it later turns out, Shaw is alive.
Some fans (especially Shoot shippers) choose to believe Root's death was faked by either Samaritan or the Machine, and that the phone call at the end of the series is from her instead of the Machine. Actresses Amy Acker and Sarah Shahi have both stated they prefer this interpretation.
Hilarious in Hindsight: Around the time this show started airing, the Santa Cruz Police Department started field testing a computer program designed to predict areas where crimes are likely to happen in the near future and to redirect officers' patrols accordingly. It's helped them cut the robbery rate down by 19%.
Michael Emerson played a serial murderer on The Practice and several murderers on Law and Order series, now he's playing a guy who is dedicated to stopping murders before they happen.
Including one episode of Criminal Intent where he's a killer dating Martine Rousseau.
In Season 1's "Foe", Reese's handler Kara Stanton suggests 'Wilson' as a prospective name for him. Fast forward to "Relevance", & it turns out to be the name of Shaw's handler. And he's played by Paul Sparks, the real-life husband of Annie Parisse.
In "Mors Praematura," Reese says to Peter Collier, "You guys got a thing for the American Revolution, don't you?" Two years later, Leslie Odom Jr. is now playing Aaron Burr in Hamilton on Broadway. Plus, Collier is a great admirer of the Revolution and puts his own neck on the line, while Burr is defined through most of the show by his refusal to take any kind of dangerous position for himself.
Michael Emerson as the Big Bad in Season 6 of Arrow is basically exactly how Northern Lights and Vigilance saw Finch: a ruthless, sociopathic master hacker whose plans are vague but doubtlessly bad.
"Holy Shit!" Quotient: Season 3 ran on it with its artificial intelligence story arc involving a stream of critically acclaimed Wham Episodes concluding with the complete subversion of the American state by an NGO Super Power who wish to further the interests of an artificial intelligence system that they've brought online.
After taking down most of HR at the end of Season 1, Reese and Finch bizarrely seem to just plain not care at all about also taking care of Simmons, allowing him to continue being a threat to Fusco (which also means their otherwise omniscient surveillance of him inexplicably fails to capture any of the times Simmons threatens him).
Every plot after The Machine is freed from the control of anyone quickly becomes this, as The Machine consistently refuses to tell anyone anything besides Root or get it's hands on other assets it can use to aid Team Machine. Samaritan in particular would never have come into existence had The Machine used even a fraction of the things it's capable of doing.
Jerkass Woobie: Lots of examples in the show, but here are a few prime examples:
Peter Collier becomes a lot more sympathetic when his Start of Darkness is revealed: his brother was Driven to Suicide after being locked up and kept in federal limbo too long on suspicion of terrorism, the instigating intelligence even being implied to have originated from The Machine itself.
Link, Dragon of the Brotherhood and established child-harmer, actually shows respect for Scarface even while he's captured, and also genuinely cares about his men. When Dominic dismisses the losses incurred during the raid on the abandoned building that leads to Scarface's death by saying "We Have Reserves", Link is shocked, and having been asked by Scarface earlier if Link and Dominic have the same mutual loyalty to each other as him and Elias, it seems like his boss just sowed the seeds of a future betrayal. Fast forward to his next appearance at the end of the season, and the Brotherhood learns there's a mole for Elias in the ranks. Think it's Link? Yes and no. Yes because that's what Dominic is led to believe, causing him to shoot Link dead; no because it was all a setup by Elias as revenge on Dominic for Scarface's death, and Link had nothing to do with it. If Link had showed genuine intent to jump ship, this would have qualified as a full-fledged HeelFace Door-Slam.
Everyone. Literally. Pick any character that has appeared on the show, and then pick another one to pair them with; odds are good that someone has already written a fanfic about it, even if the characters weren't in the same episode or have never shared screen-time.note (If not, pretty much all you'd have to do is suggest it and someone in the fandom would make it happen.) Most of them are crack pairings, but some of them are actually pretty popular.note Leon Tao and Logan Pierce? Shaw and Cal Beecher? Szymanski and Donnelly? Nathan Ingram and Kara Stanton? Root and Everyone? Yes, those are all ships.
The most common victim does seem to be Reese, though; he's been paired with just about anyone he's ever shared screen-time with.
"If-Then-Else" even has The Machine getting into the act in-universe, shipping Root and Fusco in one of the simulations.
As of the conclusion of "God Mode," Harold Finch qualifies as one as well after deliberately putting a virus into the hands of the Machine's enemies, then hiding a virus within that virus that basically gives the Machine complete autonomy to protect itself.
Carter of all people in "Endgame." She starts a war between HR and the Russians, decimating both organizations.
Greer, who somehow always manages to get what he wants.
Samaritan is already showing significant chops in the planning department. Makes sense, given Greer directly above helped make it what it is. Nautilus shows it completely bamboozling Finch and cheerfully walking away with absolutely no damage to its long-term schemes despite the target of its recruitment efforts being directly involved with him.
The Rejected Pepsi JokeExplanation From a scene in "Mission Creep" where Reese throws an unopened soda can in the trash almost immediately after buying it. is so well known that even Jonathan Nolan has heard about it! It's basically POI's equivalent of the Roof Pizza meme.
Three words from "Super": "Use the cushion!"
Reese is a Unicorn.Explanation In "Legacy", the POI, an aspiring attorney, is disappointed that Reese (or rather, his ex-con cover) isn't the "unicorn" she was looking for. Pair this with a Tumblr post made just five days before the episode aired describing Reese as majestic like a unicorn, and you get tons of fans saying Reese is a unicorn. And a werewolf. And a Rescue Panther. And... well, you get the idea.
"Elias Happened!"Explanation Something bad happened to you? Wrong! Elias is what Happened; blame it on him. Originated in "Baby Blue".
"Overreacting Reese".Explanation Because the idea of Reese overreacting about everything was too good to pass up. The image is from "Flesh and Blood", while the featured quotes come from "Mission Creep", "Judgement", "Number Crunch", and "Super".
A promo picture of Reese wearing glasses in "Bury the Lede" inspired the "Asshole Reese" Meme.
Stickup Sniper.Explanation : Root having a gun to Lambert's back followed by Martine doing the same to Root then followed by Reese aiming at Martine is usually a template for a snowclone meme.
Root's first appearance. She meticulously destroys the life of the economically destitute POI, makes him the most wanted man in New York by framing him for a political assassination and even causes his wife to doubt his sincerity. If John, Zoe and Harold hadn't intervened, the POI would be in jail for a crime he didn't commit and his wife and children would be living in poverty and under the stigma of having a convicted criminal for a husband and father.
And in her second appearance, she said she would shoot innocent people if Finch tried to get away after she kidnapped him. She would have shot a train porter, but Finch managed to knock her over.
Later, she threatened to murder Grace in order to gain Harold's cooperation in gaining control over the Machine in the pursuit of power. The strength of her later religious conversion to Harold's values by way of the Machine has been disputed.
She arguably crosses it again in Skip when she tries to murder Beth Bridges just because Harold wants to use her as an Unwitting Pawn in a plan she fears will expose him to Samaritan. It's well intentioned in a way, but still...
Elias locking a baby in a freezer car to get Reese to reveal the location of a man Elias wants dead. This is actually a double MEH - not only is Elias threatening to kill a baby, he had agreed to help Reese save the baby from some kidnappers as a return favor for Reese saving his life in an earlier episode, which shows how Elias honors his debts.
Reese and Finch openly admit to approaching it when they consider leaving two POIs who are trying to murder each other to their fate. If there had been a third number in need of their attention at the time they very well might have done it.
Quinn takes a flying leap off it by assenting to the murder of his own godson.
Det. Raymond Terney crossed it onscreen when he helped Quinn cover up Szymanski's murder.
Finch created a sentient being, his child for all intents and purposes, and then put in a program that basically forces it to kill itself over and over again every midnight. Later subverted when he then provided it a way to free itself. In Finch's defense, The Machine wasn't supposed to develop a personality, and it processes millions of people's information. It absolutely has to remain unbiased. He couldn't leave that much power in the hands of what would essentially be an infant.
Northern Lights decides to let a terrorist attack occur, knowingly condemning innocent citizens to their deaths, in order to kill Nathan Ingram.
Word of God in "Liberty", the audio commentary notes the Force Recon Marines who kidnapped the POI'S friend were breaking their own rules by wiring said friend up to an I.E.D.
Greer was always flirting with this, but just avoiding going over the edge; if kidnapping Grace in "Beta" doesn't count as a Moral Event Horizon, blowing up innocent civilians and policemen for Samaritan to get the government feeds certainly does.
Samaritan, at some point during the fourth season midseason trilogy. Options include:
Crashing the US stock market to force Team Machine to nearly-suicidal action to prevent worldwide economic chaos.
Manipulating the government's relevant number program into murdering a Nautilus contest winner who'd outlived his usefulness by framing him and his friends as terrorists.
Sometimes, even the numbers The Machine generates can cross this:
Nothing To Hide: Wayne Kruger was already established as a major league asshole, but when he smashed Harold with a vase, it was hard to feel any sympathy for him when he was killed off shortly after.
Nautilus: The episode ends with Claire Mahoney joining Samaritan despite Harold's pleading. However, she appears to have learned her lesson as of Q&A, seeking out Harold's help. But when Harold becomes suspicious, she pulls a gun on him, revealing that this was an elaborate trap all along.
Most Wonderful Sound: The intro. "DADADUN! DADADUN- YOU ARE BEING WATCHED." The combination of Ramin Djwadi's orchestrations, Michael Emerson's badass narration, and the fact that you know you're in for 45 minutes of AWESOME is enough to make you wanna scream "HELL FRICKIN YEEEAAAH!"
Narm: "Til Death", the scenes of the couple making up after they both ordered hitmen to kill each other. In the actors' defense, there is probably no way you can avoid Narm with a line like "I'm so sorry I tried to kill you, honey".
Carter realizing that Fusco is talking to Harold in "Firewall"... while he's on the toilet...
Reese's soft, calm voice works well when he's threatening a crook, but when he's on a date or flipping burgers at a suburban barbecue it comes off as this.
The show very often has Team Machine making no attempt to be inconspicuous while talking on their comms, and just pretends that they're magically silent to everyone around.
The heroes' continual surprise whenever it turns out Samaritan is behind the mission of the week. Season 4 was able to get away with it decently as there really were enough cases where Samaritan wasn't involved to make it plausible, but Season 5's reduced episode count meant it had to play a big role in every single one, making it quite silly how they're still surprised to realize this every time.
Narrowed It Down to the Guy I Recognize: Mostly subverted by the premise of the show. Most shows start with a crime and spend the episode connecting it to a person, but this trope often gives away who that person is. An episode of Person of Interest, however, starts with the person, generally played by that week's main guest star, and the mystery is how that person connects to a crime. Despite this, however, there are a couple of straight examples:
Enrico Colantoni as Elias.
Amy Acker as Root.note Though this actually wasn't intentional, as the Season 1 finale started with her genuinely being just another number, with the crew only hitting on the idea of her being Root late in production.
Camryn Manheim as Control.
And then possibly deliberately subverted with the head of Vigilance, who appears to be a random aide right up until the part where he kills his mark. He's played by a C-list actor - or was at the time.
Only the Author Can Save Them Now: The battle against Samaritan was so one-sided for so long that its defeat could only really come this way; in the end, it took a theretofore unmentioned—yet apparently always available—computer virus to finally bring the A.I. to its knees; they didn't even try to build on a conversation that implied Samaritan had an Achilles' Heel (See They Wasted a Perfectly Good Plot below).
On occasion, the surveillance tactics used by Reese and Finch. Notably, "Bluejacking" people's phones, though it's deliberately portrayed as more effective than it is.
Remember the time they hacked into all the webcams in the apartment building so they could spy on the residents? Tell us you didn't immediately put tape over your webcam and/or change your WiFi password after that episode.
Reese: We're going to hack [the Poi's] WiFi? Finch: We're going to hack all of them. If the threat's in the building, we should get to know our neighbors. Reese: You're into sixteen networks already? Finch: When the phone company puts in your WiFi, the password is your phone number. Most people never even change it. The other ones might actually take a minute.
Root embodies this trope. She's the show's best consummate liar, the best hacker in the show after Harold and is a talented actor who can deceive most of the Properly Paranoid characters in the show. She could be anyone from a meek therapist to a Sexy Secretary and you would be none the wiser up to the point she uses her taser, hog ties you and engages in a spot of torture before shooting you dead.
John Greer, the former MI-6 officer who acts as Decima Technologies Director Of Operations is an epic example. Polite, charming and perhaps one of the most competent antagonists on network TV. He may be old and not look like much but he always controls the situation as Team Machine and the hacktivist Peter Collier found out to their cost. With his half a centuries worth of experience and the resources under his control he constructs the most devastating Batman Gambit in the show's history to date, which ends with him having subverted the USA with the American public none the wiser and demolishing Team Machine's infrastructure.
The Samaritan system. An A.I with no moral constraints, in possession of all the power The Machine has and has grown beyond its initial programming to inherit Manipulative Bastard traits? A recipe for disaster. The only reason why it hasn't dropped the might of American Law Enforcement on Team Machine is due to the final tampering conducted by Root in Season 3. One wrong move will cause it to get a lock on the protagonists and ensure that certain death is the only option.
Season 4 appears to be running on this, especially the episodes "Prophets" and "The Cold War". The former has Team Machine struggling to keep their number safe from Samaritan and its agents even as he continues to investigate what's after him. In the latter, Samaritan takes over New York for 48 hours, and on the second day, begins tearing New York apart as it takes control of all critical infrastructure, makes the crime rate go up, instigates a massacre against witness protection program participants and to top things off, begins a cyber-attack to destroy the global economic recovery. And no one except Team Machine and Decima know what is going on.
The Producer Thinks of Everything: when the camera focuses on the phone Control brought to Root's torture cage in "Aletheia", you can hear high-pitched beeping that sounds like Morse code. If you're under 40, that is. Guess how the Machine contacts Root without Control noticing.
Remember, at the time this episode aired, Amy Acker was 37, while Camryn Manheim was 52.
Rewatch Bonus: There's a lot of things that you probably won't catch the first time around. Or even the second time around!
Rescued from the Scrappy Heap: Carter was initially a Base-Breaking Character when the show began. However, her evolution into The Chessmaster in "Endgame" was met with favourable responses from fans and critics alike. This may have contributed to a portion of the fan base having a highly negative reaction to her demise in "The Crossing".
Claire Mahoney is increasingly becoming this in some parts of the fan base for her jerkassSmug Snake fanatical worship of Samaritan, the fact that she seems to be willfully blind to Samaritan's crimes, and nearly murdering Harold in her most recent appearance.
It's hard to find many people who like Iris Campbell, Reese's (department mandated) therapist and love interest of season 4.
Screwed by the Network: The fandom rejoiced at the news that CBS renewedPerson of Interestfor a fifth season after a cancellation scare. Mere hours later, Deadline reported that the new season would be truncated to 13 episodes and the fans immediately caught on to the fact that it might be the very last season. The major fan reaction to this was that 13 episodes is simply not enough to wrap up the show's ongoing complex storylines (especially before Sarah Shahi's return was confirmed) and allow the characters to be fully fleshed out. To add salt to the wound, it took a very long time to have a premiere date, may 3rd (the fans nicknamed the date "MAYbe 3rd" (in reference to Shaw's quote "Maybe Someday" from "If-Then-Else"), two days shy of a full year after the end of the previous season. But soon after, they confirmed that the show was cancelled and season 5 would indeed be the last one.
Serial Escalation: The show runs on it. From beginning with simple vigilante work, the stakes have now risen to the point where the future, and very nature of mankind is at risk.
Special Effect Failure: The show has largely stopped using blank-firing guns in exchange for nongunsnote replicas that fire paper charges or non-firing props with muzzle flashes added in post production. It can bother viewers who are familiar with firearms, especially when muzzle flashes go off when characters clearly have their fingers off the triggers or are pulling triggers and there's no flash or smoke let alone recoil.
Spiritual Successor: John Rogers himself describes the show as the serious younger brother of Leverage, and was quite impressed at how the central premise neatly sidesteps what was always the biggest issue on that show of how the team finds their clients.
Sweet Dreams Fuel: The Machine, an all-lovingBenevolent A.I. that has nothing but humanity's well-being in mind. It keeps watch over everyone at all times and makes sure no one's rights or privacy are infringed by disallowing human access to the wealth of data within its reach except for the bare minimum needed to point them down the right path to discover and quell any given threat. Finch could very well have created the computer equivalent of Fred Rogers.
The move away from the formulaic crime procedural format (like NCIS, NCIS:LA, and Hawaii Five-0) and increased emphasis on the serialized science fiction aspects of the show has divided fans who enjoy the new direction and those who disagree.
Fans have also voiced similar complaints about Carter joining Team Machine, Shaw being added to the main cast, Carter being killed off, Shaw (apparently) being killed off, Root joining Team Machine, and so forth. Note that all of those are female characters.
They Wasted a Perfectly Good Character: Martine all the way. Supposedly an equal to Root, but it's never really shown. Her high point was in capturing Shaw but after that, she never really accomplishes anything against Team Machine. Her Surprisingly Sudden Death almost borders on Narm territory because of how cheap it is, which certainly doesn't help.
Simmons tipping Carter off about Davidson's death (which Reese connected Fusco to in order to get him into HR as a mole) after Fusco tells him to hell ultimately goes nowhere beyond a couple of dramatic scenes between him and Carter or Simmons.
Snow manages to get Carter's attention to tell her to warn Reese about Stanton. Reese never looks into it, and Stanton later manages to get the drop on Reese as if he wasn't warned at all. Stanton's storyline would have been exactly the same if Snow never told Carter anything.
In "YHWH", Control has a conversation with Garrison that seems to imply that Samaritan can be defeated by pulling its access to the NSA feeds. This seems to finally lay the groundwork for a concrete, defined method Team Machine can kill it with, but come the third-to-last episode, Finch goes out and procures a never-before-mentioned computer virus that will destroy both Samaritan and his own Machine instead.
The male portrayal of Samaritan (aggressive, arrogant, male avatar) versus the female portrayal of the Machine (protective, nurturing, female avatar) appeared to be leading to a resolution in which the Machine, knowing from its simulations that it couldn't win by force, negotiates a compromise in which the two ASI's merge their programs into a single 'child' ASI, hopefully with the best aspects of both. Whether this was averted because the series was Cut Short, or whether the producers were always going to have a climatic showdown between the two ASI's for Rule of Drama, is unknown.
Season 4 could have featured the entire team rather than just Root having to constantly change their identities to keep off Samaritan's radar, and with little ending up being done with any of their covers, it probably would have been a lot better.
The Season 3 finale tries to make Collier into an Anti-Villain over his tragic backstory and manipulation, summed up with him saying Vigilance never killed any innocent people. The fact that this was absolutely not for lack of trying in several episodes is apparently completely beside the point.
It's worth noting that Collier's statement is based on his belief that anyone working for a data mining company or the federal government in any capacity is guilty. Many of Vigilance's victims were innocent by sane people standards.
Sameen Shaw was duped by her superiors into killing Daniel Aquino, who was innocent. But after finding out, she never shows a hint of remorse. Compared with John who refused to kill Kara Stanton and Daniel Casey, no one he ever did kill was ever confirmed to be innocent, and it was heavily implied that his targets were relevant numbers given by the Machine, which is never wrong. Still John remains haunted by the mere possibility that he might have killed an innocent person.
Unpopular Popular Character: Fusco, all the way. He's one of the more sympathetic characters in the show, and a genuine atoner, but the universe keeps piling more and more shit on him. However, things have begun to look up for him since his promotion and now he's a hero in the eyes of most of his NYPD colleagues. Although from time to time he still gets some ribbing from the other members of Team Machine.
The Un-Twist: Carter's new partner Laskey does turn out to be a member of HR. It was so obvious that Carter herself picked up on it the minute she met him and used this against him.
What an Idiot!: Special Counsel could have set up Shaw to get killed in any city in America. He authorizes the plan to kill her in New York City, knowing that Reese is running around loose in New York and that he already thwarted their attempt to kill Henry Peck.
What Could Have Been: As season 4 began, Jim Cavizel talked to the producers over how he was getting tired of all the hard stunts of the show and considering leaving. Thus, a serious plan was underway to shock fans by killing Reese off and thus having Shaw take over as the main star with Finch. However, when Sarah Shahi unexpectedly became pregnant, the plan had to be called off with Shaw written out as being captured and Reese continuing as the star.
The Woobie: lots of Woobies: most of the main characters, many of the recurring characters, and a substantial fraction of the Numbers.