The Spear of Destiny has been taken from the United States by The Axe yet again and stored in Hitler's bunker. The bunker itself is located beneath the Chancellery in Berlin - it has been expanded and permanently sealed off, except for an elevator to the lowest level.
The Nazis are using the Spear's power to peek into the future and gain knowledge of advanced weapons systems, which they try to develop throughout the complex.
The ending text of Episode 2 of Wolfenstein 3D (and the Wolf3D hintbook) states that Hitler left his bunker fleeing to the Reichstag after the events of Operation: Eisenfaust, where he Blazkowicz chased him down and killed him.
The Spear of Destiny Hintbook re-accounts the backstory from the manual to the game, concerning Hitler's plans to take the Spear of Destiny from Versailles, France, and use it to win the war. It ends with a reference to the Fuhrerbunker, stating:
On April 28 Allied soldiers entered Nuremburg and took the Spear of Destiny. On that same day, Hitler commited suicide in his bunker in Berlin. The Third Reich Ended. (how this reconciles with the events of Wolfenstein 3D is unclear, since it kind of places B.J. in both places practically at the same time). Historically April 28 was the marriage of Eva Braun and Hitler in the bunker, and suicide occurred on April 30th.
- Computer Technology Labs: The Nazis would need silicon microchips and computers in order to run their futuristic weaponry. Therefore, this lowest area of the bunker complex has been dedicated to manufacturing these delicate devices. The exit is guarded by the mentally unstable Submarine Willy.
- Laser Guidance Systems: The Nazis are working on advanced weapon guidance systems, which would be used in anti-aircraft missiles and assault helicopters. This technology is also the first step towards developing satellite-based weapons. The exit from this section is guarded by Professor Quarkblitz.
- Satellite Systems: This is the largest section of the bunker complex and it is here that the Nazis work on their primary project, satellite weaponry that could strike anywehre in the world from space. This is the decisive advantage that will help them win the war, as the Allies will have no way to counter such technology. The area's exit is guarded by The Axe.
- The Fuehrerbunker: This is Hitler's old command bunker, which is now the control center for the new expanded underground complex and also the place where the Spear of Destiny is hidden, guarded by the fearsome Robot.
- Future Threat: The Spear takes B.J. into a grim futuristic place run by the UAC, filled with strange machines. Eerie radioactive vapors float around the halls, looking for hapless victims, while the Devil Incarnate waits patiently in its lair. The only way to leave this place is to defeat its master.