In 1995, the V.S.S.E., an international protection agency, helps Sercian opposition leader William McPhearson engineer a coup that overthrows a century-old authoritarian regime. Shortly afterwards, McPhearson is elected as the Sercian republic's first president. However, Sherudo Garo, the last survivor of the regime, plots to restore the old order, launching a series of attacks and assassinations that quickly destabilize the nation. As the finishing touch, Sherudo has McPhearson's daughter Rachel abducted and imprisoned in his family's castle on a remote island, demanding vital military secrets in exchange for her life. A desperate McPhearson contacts the V.S.S.E., who in turn dispatch veteran agent Richard Miller, the "One Man Army", to infiltrate the castle and rescue Rachel.
Miller reaches the island and rams his explosives-rigged boat into the castle's exterior to create an entrance. Sherudo hears the resulting boom, but his head of security, Wild Dog, assures him that Miller won't last long against his highly trained mercenaries. Meanwhile, Miller makes his way to the main courtyard against heavy resistance, eventually reaching Rachel's location. She warns him of a setup before being whisked away. Miller is then confronted by Dog's chief assassin, Moz, and his unit. He defeats them and interrogates Moz, who reveals that the true hiding spot is in the clock tower. There, Miller is attacked by Sherudo, a trained knife thrower, and guns him down, only to find Rachel held at gunpoint by Dog. Angered by Sherudo's death (since it means he won't be paid), Dog reveals his intentions to blow up the castle with Richard inside and escape with Rachel. Pursuing them to the castle's helipad, Miller arrives just as Rachel manages to break free, leading Dog to shoot her. A furious Miller engages Dog in a fast-and-loose gun battle across the rooftop, during which Dog accidentally sets off his detonator, killing himself in a fiery explosion. Richard collects the wounded Rachel and escapes in Sherudo's chopper just as the rest of the castle goes up in flames.
In the PS1 version, players can also unlock a special mission known as the "Kantaris Deal", which takes place several weeks after the main story's events. Miller is alerted by V.S.S.E to the presence of an illegal arms factory in a Sercian hotel with ties to Wild Dog's organization. He is assigned to infiltrate the factory and eliminate its owner, Kantaris. Upon clearing the lobby, Miller has three different paths to his target. The first takes him through the ballroom/casino, where he eliminates Kantaris's scythe-hand assassin, Spider. He then pursues her to the swimming pool just as she attempts to escape by air. After shooting down an escort gunship, Miller damages the engines of Kantaris's ship just as it takes off, causing it to crash and explode. The second path, which can only be accessed if there are less than 22 seconds left on the clock, instead goes through the shopping mall and down into a garbage disposal. There, Miller uses a claw arm to punch a hole in the wall, allowing him to access the underground arms factory. From there, he makes his way to Kantaris's office in the Lounge and defeats her personal security droid, which then malfunctions and rolls out the window, taking her with it. The third path can be made available if Richard does not activate the claw in time. Instead of entering the factory, he goes through the parking lot. After defeating a spider-legged battle tank, Miller disables Kantaris's car, forcing it to crash. If in any of these scenarios Miller fails to take action soon enough, Kantaris escapes and the mission is aborted. (Canonically, the spin-off game Time Crisis: Project Titan takes place after the mission's failure.)