The year is 2023. Since the world is a global village, the entire world knows about the Zone and SIRCAA, where they give interviews to the mass media etc. Their research concentrates among other things, on Project X and "anomalous energy". It turns out while the illegal artifact trade/smuggling was profitable, when outside the Zone for too long, they gradually lose their properties, shrivel etc. SIRCAA is working on restoring them, and while their rhetoric is noble, they seem about as trustworthy as your average mainstream politician/corporate CEO.
Since killing ukrainian soldiers is rather passe, the "Military" is now an international force guarding the perimeter/Wall, looking more like Trump's wet dream than Cordon's post-Soviet checkpoint. SIRCAA itself builds an HQ with an aesthetic of Arasaka tower from Cyberpunk.
You play as Skif (reference to Scythians), who is a martially skilled mercenary or something, but it's his first time to the Zone. He arrives with Professor Hermann from CoP there, because 1) his home was destroyed by anomaly
way outside of the Zone's borders (similar to a so-called Second Carribean Accident, where an outburst from Noosphere also appeared there) and 2) he's in possession of a MacGuffin in form of such shriveled artifact, now a dull grey rock. When at first he tries to restore it, he gets jumped and robbed by unknown assailants. After that you wake up, blind dog chews your leg etc. and meet Richter, who is a mentor to Skif about the Zone's peculiarities and your bro throughout the game.
The plot proper centers around Skif's allegiance to one of 2 factions.
The first is Varta (Ward), led by that bald General Kornushov. They are the Zone's police and guards to SIRCAA's white collars.
The second is Iskra, led by Scar. They evolved from 4-man group from CoP into Clear Sky v2. and are more like Freedom to Varta's Duty, I guess. They are also employed by SIRCAA, although with mutual mistrust. All of that gives everyone an impression they're up to something misguided or shady.
Anyway, since Varta is the Zone's official police, Duty gets sidetracked into Skyrim Civil War with Freedom all around the Zone. Mikluha returns to Freedom, and (Freedom) takes the Rostok, while Duty goes north-east into Concrete Plant. I've seen Zulu starting some side-quest placeholder there. General Voronin also returns, and this time, nothing will stop Duty on its glorious march towards saving the planet.
The Zone itself includes all of the locations from the trilogy (some rearranged) and a lot of new ones, some of them being previous cut content, like Generators or that geological anomaly from Clear Sky's artwork (named Malachite).
New factions include:
Noon - Strider's own faction of "good" Ex-Monolithians. There are enough of them around the Zone, and not all take it all that well.
Flame - an Antifa offshoot of Freedom. They got pissed Freedom is on NATO's payroll and formed their own anarchist radical faction.
Degtaryev forms Degtaryev Corps in Yanov, Jupiter.
While Scar is back, Limansk will be a DLC