I'm on a 'humanity heck yeah' kick. Does anyone know of any non-conversion bureau stories that have the ponies being antagonistic toward humans, and posing a potential threat to our world?

7783184
How's this one?
Uncommon Ground
It's about the United States vs mostly canon Equestria

7783194
I think I've encountered this one before. But thanks.

7783195
Welp, here's a second one.
Revenge is a Dish Best Served Cold
It's set in a universe where a space aged human encounters Equestria. If my memory serves me, this brings more humans into conflict with Equestria.
This is the second of two stories. The first focuses more on what the human does with no support from back home.

I think I could have read a few, but those are much too few and far in between.

I don't think I have many stories about a singular human vs ponies, or at least forgotten, but the closest I got is a metro 2033 crossover about a human and a changeling in pretty much a hostile Equestria, trying to return home.

Reciprocity: A Metro 2033 and MLP crossover

As for the whole of humanity vs ponies, I got even less. The closest that resemble that is a human Fallout 4 crossover, but with ponies sprinkled in. The ponies joined with the Chinese against the changeling that joined the US. Semi-spoiler: the story takes a while, but it was mentioned thay it didn't end pretty for the ponies during and after the war.

Vault Dweller

Another is about a group of young humans turned changelings, in a very anti-changeling world, and they have smart phones, antenna, jeep, and a shotgun/rifle. But that is as far as HFY as it gets, for now anyways. Somewhat early-mid spoiler: They find out that other human-turned-changeling ancestors were there before them.

Don't bug me

You'll more likely to find HFY stories leaning towards the non-violent side. But even then, it is still little and not focused on as much... which I could recommend one on the contrary because it is that good of showcasing humanity's beautiful and chaotic mind!

Life finds a way