While investigating the activities of the SS Paranormal Division in Germany, B.J. Blazkowicz and Agent One have been captured by the Nazis. Agent One dies while being interrogated, but B.J. manages to escape Castle Wolfenstein's dungeon. He then fights his way out of the castle and uses a tram car to leave the area and meet up with a member of the German resistance in a nearby village.
The SS Paranormal Division under Oberführer Helga von Bulow has been excavating the catacombs and crypts of an ancient church within the village. Their sloppy precautions have led to the awakening of hordes of undead creatures, including Saxon knights, and the entrance had to be sealed off with many soldiers trapped inside. B.J. descends regardless and fights both Nazis and Undead until he arrives at the ancient "Defiled Church" where Nazi scientist Professor Zemph is conducting a "life essence extraction" on the corpse of a Dark Knight. Shortly before B.J.'s arrival, Zemph tries to talk Helga von Bulow out of retrieving an ancient Thulian dagger, but she shoots him impatiently and proceeds. This awakens a monster which kills her too. Blazkowicz fights the monster and is airlifted out, with Zemph's notes and the daggerOne of Germany's leading scientific researchers and Head of the SS "Special Projects Division", Wilhelm "Deathshead" Strasse, is preparing to launch an attack on London using a V-2 rocket fitted with an experimental germ warhead from his base near Katamarunde in the Baltics. Blazkowicz is parachuted some distance from the missile base and smuggles himself in a supply truck. Inside the base, Blazkowicz destroys the V-2 rocket on its launchpad and fights his way out of the facility towards an airbase filled with experimental jet aircraft. There, he commandeers a "Kobra" rocket-plane and flies to safety in Malta.
Eager to know more about Deathshead and his secret projects, the OSA sends Blazkowicz to the bombed city of Kugelstadt ('Bullet City'), where he is assisted by members of the German Kreisau Circle resistance in breaking into a ruined factory and exfiltering a defecting scientist. There he discovers the blueprints for the Reich's latest weapon, an electrical machine-gun called "Venom Gun" which he also procures. Blazkowicz eventually breaks into Deathshead's underground research complex, the Secret Weapons Facility (SWF). There he encounters horrific creatures, malformed and twisted through surgery and mechanical implants. The creatures have just escaped and gone on a rampage. Blazkowicz sees Deathshead escape the SWF by U-Boat, and learns of his destination by interrogating a captured German officer.
Blazkowicz is parachuted into Norway, close to Deathshead's mysterious "X-Labs". After breaking into the facility, in which several of the twisted creatures (deemed "Lopers") he encountered in Kugelstadt are rampaging, Blazkowicz retrieves Deathshead's journal and confronts several prototype Übersoldaten, towering monstrosities coated in armor, powered by hydraulic legs, and carrying powerful fixed weapons. Finally, he confronts and destroys one of Deathshead's completed Übersoldaten and kills the researchers who have developed it. Deathshead himself escapes in a rocket-plane and does not appear in the game again.
After studying the documents captured by Blazkowicz, the OSA has become aware of a scheme codenamed "Operation: Resurrection", a plan to resurrect Heinrich I, a legendary and powerful Saxon warlock-king. Despite the scepticism of senior Allied commanders, the OSA parachutes Blazkowicz close to Castle Wolfenstein itself. He arrives at the village of Paderborn and, after assassinating all the several senior officers of the SS Paranormal Division present there for the ressurection, fights his way through Chateau Schufstaffel, and into the grounds beyond. After fighting two more Übersoldaten, Blazkowicz enters an excavation site near Castle Wolfenstein.
Inside the excavation site, Blazkowicz fights Nazi guards and prototype Übersoldaten, and makes his way to a boarded-up entrance to Castle Wolfenstein's crypts. There, he finds that the ruined part of the castle has become infested by undead creatures, which are attacking the castle's desperate garrison. After fighting his way through the castle, Blazkowicz arrives slightly too late at the site of a dark ceremony to resurrect Heinrich I. At the ceremony, SS Psychic Marianna Blavatsky conjures up dark spirits, which transform three Übersoldaten into Dark Knights, Heinrich's lieutenants. She ultimately raises Heinrich I, who "thanks" her by turning her into his undead slave. In a climactic battle, Blazkowicz destroys the three Dark Knights and Heinrich I as SS chief Heinrich Himmler watches in horror from afar.
