This backstory is taken from the original DOS version of the game (most of the Mac Family games that have adaptations of these levels do not actually have any in-game storyline details, but only what the manual describes for the character and his motives).
Following the events of the Original Encounter (2nd Encounter), B.J. is again sent into stop Hitler's new plan. This time rumors of Operation Eisenfaust. He is captured before he is able to infiltrate Castle Wolfenstein, and thrown into the castle dungeon. After defeating Hans Grosse for the second time, he ran out of the castle and hooked up with the Underground. They informed him that the rumors were true: some hideous human experiments were seen around Castle Hollehammer. He confirmed that Operation Eisenfaust was real.
He was ordered to journey there and terminate the maniacal Dr. Schabbs before his undead armies marched against humanity. Following a long battle, B.J. stood over Schabbs fat, evil, swollen putrid body, glad his mission was finally over. All his journals and equipment would be destroyed. Hopefully, humanity would finally be safe from his hordes of hideous mutants.
Yet the Nazi atrocities continued: thousands march into death camps even as the Nazi war machine falls to its knees. There was only one way to stop this madness.
After defeating Dr. Schabbs, Hitler again was forced to flee. He had escaped to the Reichstag, and hid in his titanic Reich Bunker as the Third Reich crumbled about him. B.J. was ordered again confront him, and to assassinate Hitler, and end his mad reign. After a long battle, the absolute incarnation of evil, Adolf Hilter, lie at B.J.'s feet in a pool of his own blood. His wrinkled, crimson-splattered visage still strains, a jagged-toothed rictus trying to cry out. Insane even in 'death'. B.J's lips pinched in bitter victory, he kicked his head off his remains and spit on his corpse. "Sieg heil ... huh. Sieg hell."
The Macintosh introduced a level package with six episodes, correspondent to the 60 levels of the PC (know as the Third Encounter) alongside the Second Encounter. Although they are not a precise adaptation, with high modifications in the level format, as well adapted to its own wall and items pack. Some propositional changes such as adding the new weapons and items, or in level structure as the secret pushwall maze in E2M8.
The final level of each episode in the Third Encounter episodes bosses appear, respectively: Hans Grosse, Dr. Schabbs, Adolf Hitler (all as normal), Trans Grosse, the Death Knight and finally a Death Knight clone alongside a Trans Grosse clone. The Death Knight drops a silver key, instead of a gold key, to support the final level of Confrontation episode that contains two bosses.
The levels on DOS were all re-created in a non-precise form.