In the game's intro, U.S. Marine Captain Frank Castle enjoys a picnic with his family in Central Park. However, Frank's wife and children accidentally witness a mob killing and are murdered as a result. To avenge the death of his family, Frank becomes a vigilante known as the Punisher, who wages a one-man war on crime. The game begins in an illegal casino and the streets of the New York City, with the Punisher (optionally partnered with S.H.I.E.L.D. agent Nick Fury) in pursuit of the Mafia enforcer Bruno Costa, who ordered the killing of the Punisher's family. The chase ends with a fight against Chester Scully (a minor villain from the comics), whom the Punisher "interrogates" until he gets the information he needs before promptly shooting Scully. Still on the trail of Bruno, the Punisher infiltrates the mob's Pantaberde resort in Florida via a water duct. He breaks into a hotel and corners Bruno, who is suddenly killed by Guardroid, a robot that the Kingpin has programmed to terminate the Punisher. After defeating Guardroid, the Punisher then raids a major drug smuggling ring at a local harbor, which ends with him confronting Bonebreaker in a waterfront warehouse. After that, the Punisher attacks the Kingpin's poppy field at a cave in Arizona. The Punisher boards and destroys a freight train commanded by Bushwhacker. At this point, the Kingpin decides that he has lost enough henchmen and money to the Punisher's actions. He puts a hefty contract out on the Punisher, who is then chased by assassins from his hideout and through a forest. After defeating another Guardroid, the Punisher infiltrates the King Building, fighting his way through Jigsaw and other enemies to the final showdown against the Kingpin himself. After the Kingpin is defeated, the entire tower collapses, but the Kingpin is not found amongst the many dead criminals in the rubble.

In the game's intro, U.S. Marine Captain Frank Castle enjoys a picnic with his family in Central Park. However, Frank's wife and children accidentally witness a mob killing and are murdered as a result. To avenge the death of his family, Frank becomes a vigilante known as the Punisher, who wages a one-man war on crime. The game begins in an illegal casino and the streets of the New York City, with the Punisher (optionally partnered with S.H.I.E.L.D. agent Nick Fury) in pursuit of the Mafia enforcer Bruno Costa, who ordered the killing of the Punisher's family. The chase ends with a fight against Chester Scully (a minor villain from the comics), whom the Punisher "interrogates" until he gets the information he needs before promptly shooting Scully. Still on the trail of Bruno, the Punisher infiltrates the mob's Pantaberde resort in Florida via a water duct. He breaks into a hotel and corners Bruno, who is suddenly killed by Guardroid, a robot that the Kingpin has programmed to terminate the Punisher. After defeating Guardroid, the Punisher then raids a major drug smuggling ring at a local harbor, which ends with him confronting Bonebreaker in a waterfront warehouse. After that, the Punisher attacks the Kingpin's poppy field at a cave in Arizona. The Punisher boards and destroys a freight train commanded by Bushwhacker. At this point, the Kingpin decides that he has lost enough henchmen and money to the Punisher's actions. He puts a hefty contract out on the Punisher, who is then chased by assassins from his hideout and through a forest. After defeating another Guardroid, the Punisher infiltrates the King Building, fighting his way through Jigsaw and other enemies to the final showdown against the Kingpin himself. After the Kingpin is defeated, the entire tower collapses, but the Kingpin is not found amongst the many dead criminals in the rubble.