At the time of writing, Marvel are publishing a mini-series called 'The Marvels Project' which tells the story of the Marvel Universe at the start of World War II. Since it's inevitable that someone will eventually do the same for the end of the war I thought I'd collate what is known of the MU at that point, with as few pages as I can manage.

Before proceeding, a little background knowledge on Baron Strucker is necessary. In INVADERS #32 & 33 (Sept & Oct 1978) a young Victor von Doom, his face wrapped in bandages, is involved with the attempt by the Nazis to draw Thor to their cause. As revealed in MARVEL UNIVERSE #1-3 (Jun-Aug 1998), he has travelled from the future and while he is away from it Baron Strucker uses the unguarded machine to travel to the future. In his few hours there he steals a handful of books, including 'The Rise & Fall of the Third Reich', 'The Manhattan Project', and 'The 1950s: A Look Back'. Armed with these, and having fallen out of favour with Hitler, he decamps to the pacific where, with the aid of the Japanese underworld and funneling money and materials stolen from the Nazis, he founds Hydra. This wartime Hydra first appears in CAPTAIN SAVAGE AND HIS LEATHERNECK RAIDERS #2-4 (March-July 1968). That encounter is precised in MARVEL UNIVERSE, which features the Invaders' encounter with Hydra. By that point, Strucker is back in Hitler's good books, the Nazis unaware that while he might still wear the uniform of a Nazi officer his true alliegance is now entirely with Hydra.

page 1: This scene is probably 1944, before D-Day. It's significance will become clear later.
Marvel Universe #1
(June 1998)
page 2: FDR died on April 12th, 1945.
The Saga of the Original
Human Torch #2 (May 1990)
page 3:
Namor #10
(Jan 1991)
page 4: Strucker puts Master Man & Warrior Woman on ice before escaping Berlin and discarding his Nazi uniform for good.
Namor #10
(Jan 1991)
page 5: Thirteen days after Lt. Farrow had given them their orders, the Invaders turn up in Berlin with a lot of other 'mystery men'. This is presumably the first time the Torch attempts to assassinate Hitler. However, given that Berlin was completely encircled by the Red Army at this point and that the furthest Western troops had reached by the 25th was the River Elbe - where that very day they finally met the Russians, whose advance had taken them far the the west of Berlin - it's a puzzle as to just how the mystery men, Sgt Fury and his Howling Commandos, and what looks to be other US soldiers too, got to the city in the first place. I can't imagine Stalin allowing them access.
The Twelve #1
(March 2008)
page 6: Twelve 'mystery men' get separated from their fellows and captured.
The Twelve #1
(March 2008)
page 7: This has to be Cap's last visit to Berlin and so must be when he has his final wartime encounter with the Red Skull, as recounted by him below. It's possible the reason Cap and others were sent to Berlin at this time was specifically to stop some thus far unrevealed scheme of his. A longer version of that encounter appeared earlier in Tales of Suspense #72 and included his warning to Cap of robotic Nazi revenge weapons the Sleepers, which would awake decades later. Incidentally, the 'Grand Imperator' referred to in that final panel when the Skull wakes up in the present day is Baron Strucker.
Tales of Suspense #79
(July 1966)
page 8: After their brief incursion into Berlin, the Invaders and other 'mystery men' must have been either ordered out or driven out, but five days later the Torch and Toro are back to kill Hitler.
The Saga of the Original
Human Torch #3 (June 1990)
page 9:
The Saga of the Original
Human Torch #3 (June 1990)
page 10:
The Saga of the Original
Human Torch #3 (June 1990)
page 11: Here's Hitler's account of that last scene. His mind in a cloned body, he escapes to South America where, years later, he encounters the Fantastic Four as the Hate Monger.
Super-Villain
Team-Up #17
(June 1980)
page 12: While the Torch and Toro are facing Hitler, Cap and Bucky have their own fateful encounter with Baron Zemo at an allied airbase in the south of England. (Note: In CAPTAIN AMERICA: REBORN this encounter is relocated to the Channel Islands. Since those islands were Nazi-occupied until May 9th, 1945 there could not have been an Allied airbase on them...so, no.)
Avengers #4
(March 1964)
page 13:
The Saga of the Original
Human Torch #3 (June 1990)

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