Paranoia 2: Savior is the standalone sequel to the Half-Life mod Paranoia, which was ported to the Xash3D engine as Paranoia: The Game. Paranoia 2: Savior takes place shortly after the first game, putting the player back in the shoes of Major Alexander Kalashnikov as he continues his descent into the abandoned KROT-1 laboratory. The deeper Alex descends, the more he learns about the experiments that took place there, discovering that the monsters within must be eradicated at any cost.

Like the first game, Paranoia 2 is a horror-oriented linear first-person shooter. The player's arsenal consists solely of realistic military weapons, such as pistols, rifles, and machine guns, which can be refilled with ammo found around the environment or scavenged from enemies. First aid kits and painkillers can be used to restore lost health points, but only painkillers are light enough to be carried and saved for later. The player is also outfitted with a retractable helmet which can be used to reduce incoming damage to the head and a gas mask which is vital for traversing areas contaminated with toxic gas.

Three Weeks have passed since the defeat of the sabotage group. The Major wakes up in an abandoned hospital.

Cutting back to three weeks ago, two hours after the terrorists were dealt with, the Spetsnaz are told of the creatures from KROT-1t hat are spreading in the lower labs. The troops are then ordered to do a clean-up, and kill as many creatures as they can. After restocking on ammo, the major and his team enter the labs from the service elevators.

The Spetsnaz eventually reach KROT-1 where command orders that the labs be destroyed. Unfortunately, the virus had already spread outside of the labs and in the 3 weeks during which The Major was in a coma in the hospital from the intro, Russia had all but completely collapsed as the virus turned the infected into zombies. Thankfully The Major was given a cure during his stay at the hospital thus he did not succumb to the virus. The state of the rest of the world is unknown. Despite the fact that the cure The Major had received seems to work perfectly fine, it was not provided to the wider public, this is probably because the virus had evolved past the current cure and The Major had contracted it quite early in its weaker form.

Exiting the hospital The Major steps out in to what seemed to be a military checkpoint, however the lack of corpses or zombies seems to indicate that the checkpoint was promptly evacuated before the virus could reach it. As The Major ventures forth he comes across an ambulance with a working radio inside. The radio receives an automated message that repeats: "To all survivors, does anyone hear me?". Since the message is automated it is unknown whether there are even any survivors left. The radio message and the newspapers in the hospital seems to indicate that the city of Moscow was under full quarantine and that The Ministry of Health and Social Development claimed that they the outbreak is under control. The time of publication on the newspaper seems to indicate that society might have only lasted about a week.