So how would you write an HHaS story set in the Crystal War timeline from the episode "The Cutie Re-Mark".

As in this war:

The Idea here is that since the Crystal was is a clear allusion to World War 2, Equestria being the Western Front, This attack on the Human World is an allusion to the Eastern Front. Sombra's Operation Barbarossa. If you know the History as well as the countless memes on the subject, you already have an idea how "successful" that conquest went. . .

"Not one STEP BACKWARDS!"

Like Hitler in that scenario, Sombra now finds himself with is a Two-front war he has no hope of winning. Humanity on one side, Equestria on the other. his resources stretched and dwindling against the Human forces as he goes on the defensive.

This is a "A Human nation saving Equestria" fic as the US and it's allies enter the War and launch a counterattack on the Crystal empire. Taking the heat off of Equestria as it was clearly struggling to keep fighting in that timeline. As Applejack put it....

"And even with Princess Celestia leadin' the charge, it still takes every last pony in Equestria doin' their part, workin' day and night, to keep up the fight."

This would later on become a "Group of Humans saving Equestria" fic as a Task force is sent to apprehend or if things get nasty, kill Sombra.

Meanwhile the Human forces are breezing through, carving a path of destruction across enemy territory and knocking at the front gates of the Imperial Capital.

To set the stage, the entrance into Equus would have been of King Sombra's doing as he would inevitably learn of the existence of the Human world and set his sights on conquering Earth and enslaving Humanity to bloat his army's numbers. Instead of using the mirror, he builds a gigantic portal to the Human World and launches an invasion into that world.

He got lucky as said portal opened up smack dab in the Middle of Washington DC. For a while he was able to take the city and with the heads of state dead or mind controlled, believed he won by cutting the head off the proverbial snake and expected the rest of the American people to submit. Completely unaware of how far it's chain of command goes (if he's even aware of such a concept), how powerful and larger the US military is compared to his and the fact that red-blooded Americans, many of which own guns will not take this attack on their nation lying down.

Whatever your protagonist does in Equestria is up to the writer but the story would consistently start amidst a battle to retake the capital:

As well as recurring flashbacks of the preceding campaigns leading up to that offensive.

The retaking would not be immediate and Sombra would hold out for about two months and rapidly conquers the Northeastern Megalopolis (BosWash) before the Military would be able to gather enough of their forces to push back against the forces of the King of shadows. If Sombra were to get his hooves on a Map of the US, He would be most attracted to the Major Cities and population centers and would set his sights conquering the largest patches of light on this map.

As for why the Military would take that long to regroup and launch a counterattack? Much of our military is stationed outside our country and some of the ones in our country are still a distance away from that specific region of our country, and it would take a while for them to withdraw them back to US soil for this kind of offensive, but once they do gather them, there is no contest between both forces as the Military stomps Sombras Army of both Human and Pony mind-slaves back to DC and eventually does force him back to Equus. So while the Military is gathering it's forces, Sombra would have to deal with civilian resistance as the citizens possessing firearms would put up resistance and fight back against hordes of mind-controlled pony and human slaves as it where the Zombie apocalypse.

Upon seizing the Portal, the Human forces would launch a massive counteroffensive on the Crystal Empire and carry out an expedition into Equus and eventually make contact with the Equestrians. They would ally as they share a common enemy but it would be a shaky alliance as an air of distrust and suspicion permeates between the two sides. Especially since their way of dealing with the mind controlled ponies are conflicting. One side wants to merely subdue them and free them later on, but the other side has no qualms mowing them down with a hail of bullets. Although the Equestrians would be appalled and horrified as those enslaved ponies are friends and family, The human's justification is that Sombra left them with no choice but to shoot to kill as the situation in that world was the equivalent to fighting against a Zombie Apocalypse.

I mean this is probably what facing off against mind-controlled Humans would be like: