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The MCU Wiki article about HYDRA says that the organization, under the command of Johann Schmidt, broke away from Nazi leadership in 1943. (We see a scene related to this in Captain America: The First Avenger, when Red Skull comments that "HYDRA could grow no further in Hitler's shadow" and attacks Nazi officers with one of his newly-created weapons.)

From that point on, in the movies and Agents of SHIELD flashbacks, HYDRA seems not only incredibly powerful, but increasingly so for at least part of the war. (That is, there was a "HYDRA Renaissance" after breaking away from Hitler, before the Allies started turning the tide.)

Are there any works related to the MCU, or Marvel works in general that we might assume influenced the MCU, that comment on the fate of the non-HYDRA Nazi party? Was there a period of civil war in Germany, where HYDRA and Wehrmacht/SS forces were in open conflict? Was Hitler deposed immediately, or even killed, mid-way through the war? Were there any attempts by the Nazis to offer a cease-fire with the Allies, so they could deal with Schmidt's rebellion?

By the end of the war, was there anything left of the independent Nazi party, or had HYDRA completely taken over the Nazi war machine?

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    After Captain American disappeared, the remainder of the war proceeded as we know from actual history. – Omegacron Nov 7 '14 at 18:09
  • I'm talking about before he disappeared. HYDRA seems to have hijacked the course of the war, so I'm wondering what happened to the non-HYDRA elements as it was progressing. – Nerrolken Nov 7 '14 at 18:11
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    Ah. Unfortunately, I don't think there's an answer. In the comics (at least, the 616 version) HYDRA stuck with the Nazis until they lost the war and were then driven underground while the Nazi Party was officially disbanded. Obviously things have gone a different route in the MCU version of events. – Omegacron Nov 7 '14 at 18:14
  • There seem to be some MCU-connected comics depicting Cap's wartime experience. (Note all the events described in the linked article that aren't from the movies.) I'm hoping there is some information in there, or a similar source. – Nerrolken Nov 7 '14 at 18:17
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    I imagine we'll find out in 'Agent Carter' once it starts. In the meantime, I laid out what happened in the 616 and Ultimate universes below. So far the MCU seems to draw largely from those two. – Omegacron Nov 7 '14 at 18:49
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The history of HYDRA and the Nazi Party in the MCU does not conform to the history of the war seen elsewhere. We are led to believe that, unless stated otherwise, historical events in the MCU align more or less with actual history in our universe. Just to cover the bases, though, I'll outline what happened in the comics:

Earth-616 (Main Continuity)

In the main Marvel continuity, HYDRA is a modern terrorist organization that did not exist during WWII. After the fall of the Nazi Party at the end of the war, and Hitler's death at the hands of the original Human Torch (more on that later), several of the party's top members went into hiding from Allied forces. One of these men, Baron Wolfgang von Strucker, later formed HYDRA using his own personal funds. The organization was loosely based on a secret cabal that had existed in the ancient world but disappeared during the Rennaissance Period.

Strucker and his allies - some of who were also involved with The Hand in Japan - saw HYDRA as a counter-balance to the growing popularity of capitalism & democracy in the world. They combined their belief in Facism, Socialism, and other systems to form what would become a constant thorn in the world of superheroes - HYDRA and its various offshoots.

In this continuity, Hitler was physically killed at the end of WWII but his consciousness was saved. That consciousness was later placed into clones of his original body, and he was resurrected as the Marvel villain Hate-Monger.

Earth-1610 (Ultimate Continuity)

The other continuity which the MCU draws heavily upon is the Ultimate one. In the Ultimate continuity, HYDRA is a modern terrorist organization with nowhere near the influence, resources, or power seen in either the 616 or MCU continuities. However, HYDRA in the MCU is largely based on a secret faction of Nazis in the Ultimate universe who were, in fact, Chitauri (the Ultimate version of the Skrull).

The Chitauri faction remained loyal to their Nazi allies right up to the time that the Nazis lost the war. Their mission, however, was actually to prepare the Earth for a Chitauri invasion that was decades to come. Following the fall of the Nazi Party, the Chitauri continued to work from the shadows, eventually infiltrating S.H.I.E.L.D. itself. This arc - seen in Ultimates #1 - #15 - is largely the basis for the MCU storyline of HYDRA taking over S.H.I.E.L.D. from within.

In the Ultimate continuity, we are left to assume that Hitler apparently killed himself just like in real life. Decades later the Chitauri commander, Kleiser, commented to Captain America that Hitler was a fool and never really controlled the war at all.

Earth-199999 (MCU Continuity)

In the MCU continuity, HYDRA is originally a division of the Nazi Party specializing in science & technology and led by the Red Skull. As you stated, we see in the film how it splinters off into its own organization in Captain America: The First Avenger, plus we see in AoS and Captain America: The Winter Soldier what happened to HYDRA after the war.

The ultimate fate of the Nazi Party in the MCU, however, is neither shown on-screen nor mentioned in any supporting materials released so far. Given the "real world" approach taken by the MCU, we may have to assume that following the events of Captain America: The First Avenger, the remainder of the war played out more or less like we know of from history. Under that assumption, Hitler committed suicide as the Allies took Berlin in 1945.

That said, the upcoming "Agent Carter" series will be centered around the formation of the SSR and the remainder of the WWII era. It's logical to assume that we'll get more information on both HYDRA and the Nazis in general from that source.

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    Yes, it is difficult to answer this without knowing exactly what Agent Carter will show. The indication, however, is that HYDRA broke away from Nazi Germany, but that the war between Captain America and HYDRA was an adjunct to the war with Germany; the "official" war was still ongoing. It's likely that the upcoming Avengers film will have Baron von Strucker surviving the war with Japanese help, as he did in the comics, helping to keep HYDRA alive, for the simple reason that there's no reason to change it. And Asia would be a nice change of scenery for the MCU if anything happens there. – James Sheridan Nov 8 '14 at 10:10

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