The game takes place in the year 2015, ten years after a deadly man-made virus (Spontaneous Genome Degeneration Syndrome) kills billions across the planet. The initial protagonists are four soldiers who have spent the last decade in a bunker at a Russian Kalinina military base where they were stationed. What greets the survivors initially is a barren world populated by sporadic groups of survivors. Every community is self-sustaining, with trade organized by the Seeker Guild. Seekers are people who scavenge pre-catastrophe (referred to as Old Time) equipment from ruined cities, "from sour drops to tanks". It is also revealed that after the disaster, central society became non-existent, with territories being controlled by gangs; apparently the area where the group's base was located was the territory of the Slingers, a group of thugs and thieves who have started to capture and kidnap people lately.
After securing the allegiance of a Seeker, the group took control of a nearby town and its radar station, improving their equipment with scavenged weapons. They also interrupted another kidnapping and busted up the Slinger base nearby, securing vital intelligence. The purpose of the kidnappings became clear: the Slingers were trading in human lives. A major slave market was located in New Boston, which the group wiped out and freed the slaves. They also paid a small visit to the Slinger headquarters nearby, killing their leader and permanently crippling their operations, as well as narrowly avoiding being caught in the crossfire of a gang war between the Claws and The Final Revolution, descendants of the Mafia and the Russian military, respectively.
The protagonists acquired intel about a secretive group of highly trained and heavily armed soldiers and scientists, known as NOAH. Their operations and location were a complete secret with only the local Seekers knowing the location of their laboratories. To gain this information, the protagonists intervened in the gang war in Bergstadt, joining one gang and wiping out the other (the choice is up to the player). However, the defeated gang retreated first to Smolensk, then besieged the nearby NOAH base. Although the protagonists broke the siege, another disaster was narrowly avoided as the gang attempted to deprive NOAH from power by shutting down the nearby nuclear plant, unknowingly starting a meltdown.
The leader of the local NOAH forces, Prof. Vlamidir Czeko gave the group minimal info: they were extensively researching SGDS in the hope of finding a cure, but so far nothing worked. They are suspicious of a group of monks known as the Children Of The Undying Child. The COTUC was a relatively insignificant gorup of religious fanatics who gained the attention of the media through their mass suicides. Suspiciously, nearly all of them survived the SGDS-catastrophe and seem to be benefited from it, as they used the past ten years to research advanced technology.
To get more information, the protagonists infiltrated a COTUC monastery protected by crawling mines: anti-tank mines capable of subterranean movement and are attracted to vibrations caused by surface movement. With clever use of "thumper baits" (devices that create vibration for deliberately attracting the mines) supplied by NOAH, they got into the monastery and secured documents claiming that a high-ranking COTUC member will arrive soon to the nearby airstrip. While the man was occupied, the protagonists installed a tracking device (removed from an inert crawler mine) in his helicopter, thereby tracking him back to the COTUC headquarters. When they got back to the monastery, the local COTUC spokesman offered them the chance to join forces. At this point, the storyline converges into two paths.
If the player chooses to help the COTUC (talk with the monk), the protagonists accept a mission to infiltrate a NOAH compound and get vital intelligence from the COTUC spy. The intelligence came as a shock to the group: NOAH was responsible for creating SGDS and distributing it through the world in order to develop and sell the vaccine at a high price (in fact, Czeko was the chief scientist of the project). Obviously, the vaccine wasn't completed and billions died as a result. Finally, the joint protagonist-COTUC taskforce raided and destroyed the central NOAH headquarters. At the end, the protagonists found themselves surrounded by COTUC forces who ordered their surrender. The leader of COTUC, only referred to as HE (though actually it is SHE) arrived and gave the group a Hobson's choice: either surrender and be transformed into Death Knight cyborgs, or go down fighting.
If the player chooses to oppose COTUC (kill the monks), the protagonists follow the tracker to the central COTUC base. Because security was tight and everyone was searched at the gates, they resorted to subterfuge: since they couldn't bring any weapons into the compound, they disguised themselves as COTUC monks coming to pray at the temple. Ultimately though, their identity was discovered and they had to fight for their lives. With crafty use of airstrikes and weapons found on site, they managed to not only break the strength of COTUC, but also prevented them from releasing SGDS to get rid of the intruders. It was also discovered that the COTUC research effort about the virus was brought to fruition: not only they found and synthesised a cure, but they also perfected SGDS to become an even more potent toxin; people infected by it will die in agony in a matter of minutes.
Finally, COTUC was cornered into their own headquarters. Although the central temple was defended by lots of Death Knights, the protagonists eventually prevailed, as NOAH caught wind of the operation and sent in a small army of reinforcements to help out. In addition, they found a group of disassembled Death Knights, with a commander among them. From his dialogue, it is clear that the commander fought the brainwashing and eventually regained his sanity, leading to his "decommissioning". Although he doesn't remember what happened to him, he was horrified at what he had become and assisted the group by turning the crawler mines against the COTUC, as well as entering his former unit's self-destruct codes. During the attack, the protagonists had a radio transmission telling them that security at the home base caught a COTUC spy snooping around, radioing their coordinates to a flight of heavily armed Hind gunships who were preparing to take off; the attack was barely averted. Although HE offered an alliance and joining forces, the protagonists flatly refused.
The game has three possible endings:
- If the player surrenders, the protagonists are transported away and transformed into hideous Death Knights. Their only hope is that eventually they will be able to break through the brainwashing and get revenge.
- If the player fights back, everyone is slaughtered. Maybe someone else will rise up and win against the COTUC in the future.
- If the COTUC temple is destroyed, it is remarked as the first step of humanity towards restoring civilization. Although many people fell, their sacrifice was not in vain.
The central question of the game is who is the greatest evil: the gangs who rule the land unfairly but has nothing to do with the disaster; NOAH, who created the virus and is responsible for the deaths of billions but are now trying to correct their mistake; or COTUC, who are using the virus for their own nefarious purposes ("Test of Faith": people are given the SGDS virus and those who demonstrate unwavering loyalty are given the antidote, the others die), as well as benefiting of the people's misery to increase their own power?
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