June 6, 1996.note A mysterious explosion destroys the Chernolton research facility near Moscow. Lucifer Alpha, a powerful biological weapon under secret development there, is released into the atmosphere, creating a deadly biohazard. Carried by the trade winds, Lucifer Alpha spreads throughout Eastern Europe and Eurasia, destroying 80% of the populace. Half of the world's people die. The greatest biohazard in history later becomes known simply as "The Catastrophe". But at this time, who could have possibly imagined that the ultimate biohazard wouldn't occur for another half century? 50 years later, mankind faces its greatest crisis, the appearance of a mysterious android lifeform. Its purpose and origin are unknown. Is it a new form of weapon? Or perhaps, an invasion from some other world? They appear during winter killing humans, and infiltrating society by taking the place of their victims. Employing an artificial skin, they can sweat and even bleed. Part organic, part machine, they're almost impossible to distinguish from those they kill. As they steal their victims' bodies in order to take their place, these mysterious invaders become known as "Snatchers".
The player takes on the role of Gillian Seed, an amnesiac who begins his first day as a J.U.N.K.E.R. Upon arriving at J.U.N.K.E.R. headquarters, he is introduced to Mika Slayton, Chief Benson Cunningham, and the engineer Harry Benson, who presents him with his robotic navigator Metal Gear, and his blaster. Soon after, Metal Gear receives a distress call from another J.U.N.K.E.R., Jean-Jack Gibson, who tells him that he has cornered a suspected Snatcher and is requesting immediate backup. Gillian and Metal Gear then take their turbocycle to the abandoned factory where Jean-Jack made the call, but upon their arrival, they immediately find Jean-Jack decapitated and Jean-Jack's navigator Little John destroyed, but not before recovering Little John's memory chip. While Gillian and Metal Gear are investigating Jean-Jack's corpse, two Snatchers secretly make their escape and Gillian and Metal Gear flee from the factory before it explodes after fighting off insectors, spider-like robots controlled by Snatchers.
Upon arriving back at J.U.N.K.E.R. headquarters, everyone is devastated over news of Jean-Jack's death. Gillian consoles his comrades before heading to Gibson's house, where he speaks with his daughter, Katrina. Using a floppy disk, Gillian uncovers critical information regarding the identification of Snatchers. Due to their artificial skin being unable to cope with ultraviolet rays, they have to operate at night and wear sunscreen at all times. Gillian also meets an informant of Gibson's, named Napoleon. With the information provided by Napoleon, Gillian heads to Plato's Cavern and Outer Heaven, a nightclub that served buffalo meat. While at Outer Heaven, Gillian asks one of the strippers information of the man who killed Gibson, then uses the information to run it through the computer at J.U.N.K.E.R. headquarters. They find two suspects: Ivan Rodriguez and Freddy Nielsen.
First, Gillian and Metal Gear head to Ivan's apartment. When they attempt to question Ivan, Ivan suddenly comes out with a gun, forcing Gillian to shoot and disarm Ivan. Gillian then interrogates Ivan, only to find that he's not a Snatcher, but since he's in possession of an illegal drug, Gillian has Ivan arrested. Gillian then proceeds to Freddy's apartment, where he interrogates Freddy's wife Lisa about Freddy being a Snatcher. Lisa is revealed to be a Snatcher, and Gillian kills her after a fight. When Gillian and Metal Gear proceed to leave, the light in the bathroom suddenly turns on, forcing them to go back. When Gillian attempts to figure out what happened, he is suddenly attacked by Freddy; Gillian is very nearly killed before being saved by the timely intervention of bounty hunter Random Hajile.
With the information from the floppy disk and from Random, Gillian is assigned to investigate the illicit hospital which is believed to be the Snatchers' lair. In the memory chip received from the remains of Little John, the last image recorded was that of a neon sign with the words "Hospital Oleen". Gillian once again seeks out Napoleon, who tells Gillian that he knows of an Oleen hospital. Upon arriving at Oleen, it turns out to be a veterinary clinic. Gillian and Metal Gear assume that the sign from Little John's memory chip was broken, forcing them to find more clues about the hospital.
Suddenly, Gillian and Metal Gear receive a distress call from Mika, who tells them that Katrina had been in a panic and was looking for them. Gillian immediately rushes back to Gibson's house, only to find the place ransacked and the Gibsons' dog Alice killed. Gillian and Metal Gear attempt to search for Katrina in some of the places they know, only to yield no results. They then decide to go home to Gillian's apartment, but they find that someone is there. They find Katrina showering in the bathroom, and she sprays Gillian in fright. Katrina later explains why she is at Gillian's apartment and why the Snatchers raided her home, as it turns out she found more clues. With Katrina's help, Gillian and Metal Gear find out that the Snatchers' hospital is Queen's Hospital.
Gillian and Metal Gear arrive at Queen's Hospital, which appears to be a dark, abandoned building. While investigating, they find a picture of Russia, and a patient record written in Chinese. Gillian decides to seek out Napoleon again, who is revealed to be fluent in Chinese, in order to decode the patient record. Upon meeting at Outer Heaven, they find that the patient record is a puzzle in the periodic table, and decodes the message, discovering the patient's name to be Benson. Gillian immediately rushes back to J.U.N.K.E.R. headquarters, realizing that the Benson could be referring to either Harry or the chief. However, neither Harry or Cunningham are at the headquarters, and finds a message from Harry saying "face to face". It turns out the message is referring to a picture in the chief's office and an optical illusion, showing both a vase and two faces. In the chief's office, Gillian finds a painting of Red Square in Moscow. As they attempt to find the chief, believing him to be a Snatcher, Gillian and Metal Gear receive a call from Jamie Seed, who tells them that Queen's Hospital has a basement.
As Gillian and Metal Gear drive back to the hospital, they find that the turbocycle has been sabotaged, but fortunately, Random once again arrives to their rescue and Gillian and Metal Gear jump aboard Random's motorcycle just before the turbocycle crashes off the curve. Upon their arrival at Queen's Hospital, they find the basement Jamie had mentioned and begin to investigate. They eventually arrive at the Snatchers' morgue, and identify the four corpses: Freddy and Lisa Nielsen, Chin Shu Oh, the director of the hospital, and most shockingly, Benson Cunningham. Suddenly, the group is confronted by Chin Shu Oh and several Snatchers, but before they could kill the group, Random detonates himself, destroying the hospital and seemingly killing Chin Shu Oh just as Gillian and Metal Gear escape through a ventilation shaft.
In the air duct, Gillian and Metal Gear deduce that the Snatchers have used the shaft to travel from place to place. They go further down to an abandoned subway rail, and look for an exit. They then climb a latter, and find themselves back in Freddy's apartment. They conclude that this was how Freddy arrived back home without them seeing. After leaving the apartment, Gillian calls a taxi to get to J.U.N.K.E.R. headquarters. However, the driver is revealed to be Chin Shu Oh, who was revealed to have barely survived the explosion and was waiting to ambush them outside, only for Gillian to quickly kill him. Gillian then commandeers the taxi to head back to the headquarters.
Upon their arrival, Gillian and Metal Gear find that the place had been attacked, and find Mika unconscious in the pod. When she comes to, she tells Gillian that the last time she saw Harry, he locked her inside the pod before heading off after Cunningham. She also warns Gillian to be careful with Cunningham and to look for Harry. Gillian rushes in and finds Harry mortally wounded. Harry tells Gillian that he discovered that Cunningham was a Snatcher, but he was no match for him, and Harry dies in Gillian's arms. An enraged Gillian then becomes determined to get revenge on Cunningham, telling Metal Gear that should Cunningham kill him, he must take Mika and run and blow up the headquarters. He searches the headquarters for Cunningham, only to find that he had taken Mika hostage. Gillian guns down Cunningham, and in his dying moments, the chief tells Gillian that Queen's Hospital was nothing more than a maintenance facility for the Snatchers, and that they have comrades operating throughout the city. Just then, Gillian receives a distress call from Jamie, who tells him that she being held in the "Kremlin", but the call is abruptly cut off by a Snatcher, ending the act on an ominous cliffhanger.
Gillian, Metal Gear, and Mika go over everything that had happened up until this point, discussing the Snatchers' weaknesses, those who have been discovered by the Snatchers, and the mysterious information gathered. As it turns out, there are actual links between the Snatchers and Russia, and it's revealed that the Snatchers all consider Russia their home. Metal Gear also knows all about Gillian and his past, that he and Jamie were found cryogenically frozen in a Russian facility near the spot where the Catastrophe had occurred. There was another pod, but it was empty by the time it was found. As a result of the cryogenic suspension, Gillian and Jamie had suffered from severe amnesia, and after moving to Japan, Gillian had subsequently became a member of the J.U.N.K.E.R. squad in order to regain his lost memories. They also find out that Harry Benson was Gillian and Jamie's son.
The three attempt to find the place where all the Snatchers have gathered in Neo Kobe. They conclude that it's in an area near the Ina River where the Snow 9 is still concentrated, and a place easily accessed through the tunnels. They find out that the Snatchers' main headquarters is an abandoned church, which seems to line up with the Moscow river. Gillian and Metal Gear rush to the church. But time is running out, as the Kyoto Summit discussing the Snatcher problem is coming together, and that in approximately three hours, all J.U.N.K.E.R. activity will be dissolved due to the chief's death. At the same time, there's also a vote being placed on whether nukes should or should not be used to level Neo Kobe to put an end to the Snatchers.
When Gillian and Metal Gear arrive at the church, they find it completely empty. They see a portrait of a man at the alter called "Modnar", and he resembles Random Hajile. They proceed further into the church, and uncover a factory where Snatchers are prepared to act as humans, finding data to snatch many world leaders as well as Gillian himself. Gillian tells Metal Gear to head off to warn the delegates and convince them to give Gillian more time. Metal Gear obliges and Gillian heads off to find Jamie. After fighting his way through super insectors and Snatchers, Gillian proceeds to the final chamber where he finds Jamie. Jamie reveals that she got her memory back, and that she was forced to work on development for the artificial skin for the Snatchers with Professor Modnar. Jamie also tells Gillian that the reason she had worked on the artificial skin was because she was blackmailed that they would threaten Harry's life if she didn't comply.
Another man reveals himself at this point, an old man in a wheelchair named Elijah Modnar. Elijah explains that he had captured his father in order to get help to perfect the Snatchers. He tells Gillian and Jamie that they were recruited long ago on the project, and that he, Jamie, Elijah, and Elijah's father Professor Pettrovich Modnar were involved in a top secret experiment taken under by the Soviet Union 50 years ago during the Cold War, which was designed to assassinate and replace world leaders. Elijah worked on the project because he had loved Jamie, and that she was his motivation. Later, Gillian was hired for the project to work on the psychological properties for the Snatchers, and at one point, he had fallen in love with Jamie, and soon married and had a child. Elijah was enraged at this, and as a result, plotted to unleash Lucifer Alpha before taking Gillian and Jamie to join him in cryogenic freezing. He originally planned to awaken only Jamie and have Gillian stay asleep forever, but he ultimately couldn't bring himself to do it. As Elijah continued to work on the Snatchers, his father had created Random Hajile, modeled after Elijah in his youth and named him after Elijah but spelling his name backwards, developing a more advanced artificial skin for him and programming him to destroy Snatchers. However, using Random's artificial skin, Elijah could now perfect his Snatchers.
Just then, Metal Gear arrives, strapped in explosives, and tells Gillian that the delegates will not take action if the chapel is destroyed. Metal Gear tells Gillian that in ten minutes, a phase particle beam will strike the church, but several Snatchers activate on Elijah's command. Suddenly, Random awakens and holds Elijah by the neck, forcing the Snatchers to stand down. Gillian and Jamie quickly escape the church just before the beam fires and destroys the church.
In the aftermath, Gillian and Jamie discuss their future and are greeted by Katrina and Mika. Metal Gear is also revealed to have survived, albeit by putting his memory chip in a new body, Random having protected Metal Gear's memory chip from the blast of the beam. Having learned of a Snatcher factory in Moscow, Gillian and Metal Gear depart on a plane to Moscow to finally put an end to the Snatcher menace.
