After Engel taunts Blazkowicz with Caroline's severed head, Sigrun has a change of heart and tackles Frau Engel, allowing Fergus/Wyatt to break free and Blazkowicz to use Caroline's Da'at Yichud Power Suit to regain his strength. Frau Engel hits and belittles Sigrun, particularly on the 'treasonous passages' she read in her diary, before killing Caroline herself. She then tries to get her abused daughter Sigrun to decapitate Caroline, but the former refuses. There, Frau Engel mocks and beats him, Caroline and Fergus/Wyatt. Desperate to save his friends, Blazkowicz devises a plan to get himself captured and taken to Engel's airship fortress, the Ausmerzer, which is suspending the U-boat above water. Soon after, however, Caroline and Wyatt/ Fergus (whoever survived the events of The New Order as chosen by the player at the beginning of the game) are captured by Engel and her forces.

Blazkowicz, disoriented, handicapped and confined to a wheelchair, fights his way to Anya and Set Roth, and the three proceed to the main deck. The U-boat is attacked by Frau Engel, a sadistic Nazi commander who despises Blazkowicz for disfiguring her at Camp Belica and killing her lover, Bubi, in the events of the previous game. As Blazkowicz fades in and out during his coma aboard the Eva's Hammer (a Nazi U-boat commandeered by the Kreisau Circle), it is revealed that Anya, Blazkowicz's love interest, is pregnant with twins. Blazkowicz falls into a 5-month long coma and has some of his organs removed to facilitate his survival. After the events of the first game, in which General Wilhelm 'Deathshead' Strasse is eliminated, the Kreisau Circle retrieves the critically injured William 'B.J.' Blazkowicz ( Brian Bloom) from Deathshead's fortress before destroying it with a nuclear cannon.

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