* The main villains are Majestic 12, a globalist cabal of technocrats and scientists who are working to weld the world into a totalitarian police state under their unblinking surveillance and the jackboots of their merciless soldiers. They express nothing but contempt for laws (which their AI Icarus writes off as 'arbitrary' and meaningless), traditions (they're explicitly secular and background materials suggest they never bothered using religion as a tool, unlike their Illuminati predecessors) and human life itself (as demonstrated by everything they do in-game, in the backstory, and literally every single one of their labs; per the intro sequence they're even proud of their lack of ethics allowing them to make scientific breakthroughs in areas & ways their more moral opposition refused to consider).
* How are MJ12 taking control of the world? Why, they created and are actively spreading a plague, while secretly withholding the cure. They use the plague to kill and marginalize people they can't control (the underclass of society for the most part) and the cure to compel governments into carrying out their will, which is usually to give MJ12 members positions of power and pass draconian laws. Both the plague and the cure are made of nanites manufactured by MJ12, so whether you catch the former or willingly consume the latter, you're actually putting yourself at their nonexistent mercy. Meanwhile, members of the public who don't uncritically buy the gov't line think the plague is being used to kill off 'surplus' populations, which is indeed part of (but not the whole) truth.
* The leader of MJ12 is Bob Page: the world's first trillionaire and richest man, CEO of the all-encompassing corporate conglomerate Page Industries, and publicly a generous philanthropist who only wants to help uplift humanity. In reality he's a totally sociopathic megalomaniac who never demonstrates any benevolent intention, he just sees himself as a god and wants to make that vision a reality. Oh, and Page Industries specializes in 1) electronic communication via the Aquinas Protocol and 2) biomedical R&D through its subsidiary VersaLife. So basically, he's the lovechild of Mark Zuckerberg and Bill Gates with a good helping of demonic charisma to fool the masses.
* The US federal gov't has been thoroughly corrupted by MJ12. FEMA has become little more than a skinsuit for above-ground MJ12 ops in America, the FBI is mentioned to be running youth prisons called 'good behavior camps' with populations in the tens of thousands, and the president is paying dues to the UN over congressional objections. Washington blatantly doesn't give a crap about the people it represents and yet, despite a 35%-and-dropping approval rating, said president is implied to be clinging to power through illegitimate means according to the NSF leader you arrest at the end of the first level.
* Speaking of the UN, they're another one of MJ12's public faces and churn out propaganda proclaiming that perfect liberty requires a perfect police state with perfect(ly intrusive) surveillance, centralized control of communications and a universal electronic currency. The latter two already exist and MJ12 is working hard on the first item. In general, if MJ12 or any of its catspaws say something's good for you, they 100% do not have any good intentions beneath the rhetoric.
* Oh, and they have their own army, the United Nations Anti-Terrorist Coalition! While ostensibly a benevolent and humane peacekeeping organization, UNATCO is extremely secretive, and for good reason - besides being MJ12's public military arm, they actually employ mech-aug (cyborg) agents who are blatantly bloodthirsty psychos and encourage you to indulge in similar behavior. Even their rank-and-file grunts express a most un-peaceful eagerness to kill dissidents with lines like 'You got the right idea, cap the bastards before they get lawyers involved.' and 'A bullet to the head, now that's justice. You catch on quick.'
* But at least UNATCO pretends to be working for the public good and the majority of its members are shown to be unaware of MJ12's existence, much less their motives - they genuinely think they're doing good work, ridding the world of dangerous terrorists. The same can't be said of the actual MJ12 army which openly operates in France (and secretly around the world) and brutally puts down dissent, to the extreme of torturing prisoners and murdering entire families in their beds just because one of them criticized MJ12's actions (as evidenced by a conversation with an MJ12 trooper's family in Paris). They're well aware of what they're doing, unlike UNATCO and the cops you run into from time to time, but knowingly continue to serve MJ12 for sweet paychecks or out of genuine loyalty while the press covers up or justifies their atrocities. Amusingly, they're thought to be either some French military faction that's staged a coup or an outright EU army by the French public.
* Speaking of the press...in addition to virtually every gov't on the planet, every known media outlet is also under MJ12's thumb. Throughout the game you literally can't find even a single one that's actually reporting the news objectively and honestly instead of just parroting MJ12-crafted narratives, not even the one that seems to be anti-government (and is demonized as a future Infowars by the mainstream) at first glance. You want actual news, you have to listen to the resistance, which MJ12 has declared to be terrorists deserving extermination on sight through the fake news and their many other official fronts.
* In general, technological & social progress are depicted in a far from universally positive light - indeed it's clearly why MJ12 has come so far in the first place, and you're left wondering how much of either were organic developments and how much were steered by MJ12 or the Illuminati before them. One of the endings has you actually destroy both, throwing the world into a period literally called the 'New Dark Age', and this is presented not just as a viable course of action but potentially a moral one; the game doesn't call you a bad person or otherwise judge you for choosing this path.
* So, who dares stand against the power of MJ12? Well, obviously there's you: a vat-grown clone baby designed from the ground up by MJ12 to test their nanotech. Said nanotech also includes a function to kill you in 48 hours if you ever go against your creators.
* But then there's also the NSF and X-51 in the States. The former are a right-wing militia that rebelled because, according to the backstory, Washington has pretty much outlawed private ownership of firearms. From a conversation you can overhear in the first level and an ex-NSF bum who sells you sniper ammo upon your return to the second, they're established as explicitly religious and conservative-minded, allying with inner-city minority gangs only to pad out their depleted manpower after a decade of guerrilla warfare against the feds. X-51 is a less ideological and much more recent rebellion, the result of a bunch of MJ12 scientists and soldiers defecting from Area 51.
* In Asia, the resistance's main representative are the triads. Who are condemned for indulging in techno-piracy and selling bootleg materials to small businesses, which are all too happy to take said bootlegged stuff because it's cheaper than if they'd bought legitimately from megacorps like Page Industries and its subsidiaries. And their primary representative, the hacker Tracer Tong, is the one who gives you the idea to inaugurate a 'New Dark Age' in the first place.
* In Europe you deal with Silhouette and the Illuminati. The former are basically a Situationist International-type avant-garde revolutionary cell, so fine, not exactly based - though they still have the stones to risk their lives against MJ12, and have caused enough of a nuisance that MJ12 staged false-flag terrorist attacks to make them look bad. The latter are a more conservative, spiritually inclined conspiracy (they actually chide Bob Page for being impatient and overly materialistic, thereby failing his spiritual exercises when he was still part of their cabal, in-game) whose leaders are contemptuously referred to as 'pretentious old men' by Page himself. Also, the former ultimately prove to be little more than the latter's subverted muscle, and are outright absorbed by them in the sequel...tell me again, how effectively are the socialist Democrats like Bernie or AOC standing up to their betters in the establishment?