If you want to skip the prelude and start on the actual story, you can. For those that want to read the prelude, I tried to make it sound interesting. But be warned, the contents are very graphic. Anyway, enough said, let's get on with the story.
On the 2nd September 1945, the USA had won the war in the Pacific. The Japanese Empire was defeated. The Second World War finally came to an end. However, a new enemy would threaten the globe, and it would come from one of the victors.
The Soviet Union had suffered greatly in their Patriotic War against the Germans. Their motherland was devastated, and lost over 25 million people, men, women and children alike. Stalin vowed to not let another invader do such a thing, again. It wasn't just the Germans or the Axis that contributed to the state they left the USSR in...
Discord in complete discretion, placed all of Equestria above Finland just at a few weeks before spring ended in 1941. In Equestria's time, this was after the mane 6 defeated King Sombra, when Discord jumped infront of Sombra's attack to save Fluttershy. Anyway, Discord in his infinite wisdom thought taking Equestria to a world that's at war and have Equestria take part in it would be an even better idea to test Twilight and her friends on top of them facing against Tirek, Chrysalis and Cozy Glow. Of course Discord said nothing, as he intended on it being a test. Everypony else in the meantime had absolutely no clue what was going on other than they are all in a completely different world.
The first country to notice this land was the Soviet Union, but they had no interest. They had much more urgent problems to deal with than a chunk of land that randomly appeared out of nowhere. Stalin did send 100 thousand troops with 18 T-26's, 40 BT-2's, 20 A-32's, 25 KV-1's and a single KV-2 in Murmansk, nearest to where that land out of nowhere was discovered, just to be cautious. He also put a squadron of aircraft and artillery units on standby as well in the region.
The next country to notice was Nazi Germany, and they saw this as an opportunity to bring another ally on their side. Adolf Hitler was also informed that this land had magic, and he thought this might be the closest he'll ever get to having the Holy Grail he seeked for. Hitler sends a representative to the capital of this discovered land, to propose an alliance of mutual assistance. The diarchy in charge of the land thought carefully. They're in a completely different world they knew nothing about, and some sense of protection would be beneficial. They agreed to be in an alliance with the Germans. The Nazis began sending all sorts of military equipment to Equestria, and helped enhance Equestrian industry, forming the bond Hitler needed. He saw the use Equestria's magic could provide great assistance with plans he had later on in the year. Equestria's alliance with the Nazis made taking over virtually impossible for Tirek, Chrysalis and Cozy Glow, forcing them into a very dull long waiting game that would span for years to come.
In June, the British discovered the seemingly unclaimed territory. They thought it could provide an advantage against the axis if they occupied the territory. But luckily, one of their codebreakers at Bletchley Park found that the Germans already have control, and warned the navy just in time. This ended up saving a total of 50 thousand lives.
Before Operation Barbarossa, Hitler gave false evidence to the Equestrian diarchy that the USSR was planning an invasion from the sea. It did look like the Soviets were preparing to invade Equestria as they had military presence in Murmansk. Equestria had no choice but to believe Hitler's word, after all, he provided them equipment to defend themselves didn't he? Hitler had Equestria controlled with strings, through manipulation. Discord meanwhile realized he dug himself a deep deep hole. He can't go back on this, or it'll make everypony hate him for getting them involved in a global war.
The Royal Guard had introduced conscription, which caused the guard to go from originally 3,000 or so warriors to over a million in just under 2 months. Celestia and Luna were hesitant to introduce conscription, but were pressured to by the Germans. If they refused, they would no longer have the protection Germany granted them, or even worse, it would incline Germany to invade. When the time for Operation Barbarossa came, Army Group North headed for Leningrad, Army Group Centre headed towards Moscow and Army Group South went to head for the Caucuses. Equestria invaded by advancing through Murmansk, with the assistance of the Luftwaffe softening Soviet defences.
The results of Operation Barbarossa were the same as in the real life timeline, except Soviet losses were higher, either to Equestrian magic or German equipment given and used by the Royal Guard. But still, the Royal Guard were humiliated on the eastern front. They were practically made of a force comprised of conscripts, and the guard was suited to defend against an invasion, not to be the invasion force themselves. In one case, a single T-34 held off an entire Royal Guard regiment.
After Kursk, everypony began to really question themselves whether siding with the Germans was a good idea. Slowly, the ponies realized they were manipulated, but the damage had already been done. By the end of 1944, it was clear to Equestria that the Germans were the bad guys. There was a reason why Hitler never had anypony be part of an occupation force, to avoid the dark truth reaching the diarchy. Anypony that got a bit too close to the truth were shot in upmost secrecy, which nopony knew until the end of the war. However, the news of the concentration camps and the Final Solution did eventually reach Celestia and Luna, leaving them disgusted at what they've unknowingly aided in.
On the 1st January 1945, the Equestrian diarchy requested the allies for a ceasefire. The British, Americans and Canadians accepted the ceasefire. Equestria was fully committed to the eastern front and never directly fought the western allies. Equestria also didn't play any part in the Final Solution as the Nazis covered up their atrocities from Celestia and Luna to avoid the bond being split.
The diarchy then requested the Soviets for a ceasefire as well. Stalin said the Red Army will assist in providing a safe passage for the Royal Guard to return to Equestria. Weeks passed, and nopony from the eastern front returned.
This brings us back to 2nd September 1945. The Second World War was 'over', but the Soviets had different ideas. The west were wary of why the Soviets were still investing so much into their navy, despite their crippled economy. The Soviets had begun production of cargo ships since early 1944, and the US president at the time, Franklin Roosevelt assumed the Soviets were going to assist the US in the Pacific, and sent 300 Liberty cargo ships to the USSR.
Again, back to the 2nd September 1945, the USSR was still investing extra money into their navy. The Red Army or the Red Air Force didn't receive cuts in military spending. The USSR isn't planning an invasion of Japan.
A few months have gone by, and everyone still have no idea what the Soviets were up to. So, what were the they up to? Not only that, what happened to the ponies on the eastern front? Also, what happened to missing ponies in Equestria who had absolutely nothing to do with the war?