The assault on Strasse's facility fails. Blazkowicz is captured and Strasse presents him with a modified version of Sophie's Choice, forcing him to choose which of his two comrades will be brutally eviscerated and experimented on. After Strasse finishes with his subject, Blazkowicz manages to escape, but in the process suffers serious combat wounds. These put him into a vegetative state that lasts fourteen years. When he regains full consciousness, Blazkowicz discovers that the Allies have lost World War II and the Nazis now rule most of the known world. You spend the rest of the game as part of an insurgent cell trying to find ways to undermine the Nazi regime.
One sentiment that's been shared by a number of players is that the ending doesn't satisfy. In the final moments of the game, Blazkowicz repeatedly stabs Strasse, seeming to fulfill his vengeance quest. Yet, as he is dying, Strasse opens his hand to reveal a grenade with the pin pulled. It explodes, killing Strasse and mortally wounding Blazkowicz. Strasse dies on his own terms: self-satisfied and content in the illusion that he has contributed great good to the world by furthering technological progress and developing the master race.
It would probably take thousands of lifetimes to repay the evil some Nazis committed during World War II, to say nothing for those Nazis who, in this fictional universe, continued to perpetrate untold suffering all across the world, unopposed by any serious military threat. I'm not surprised many gamers have found the ending unsatisfying, for the secular world has no capacity to deal with extreme injustice. Only the afterlife offers resolution: punishment for the wicked and bliss for the righteous.