Alternate timelines persist.
They sorta have to, in order for time travel to work at all: Let's say you go into the past, and then change history. Alright, so assuming you can't paradox yourself out of existence, that has to mean that your original timeline still exists in some form or other. Now, however, let's say you go back again, and prevent that change from occurring, resulting in events going back to the way they went the first time around (or maybe just creating a new timeline nearly identical to the one you started with, always a strong possibility). If non-paradoxing out of existence means that your original timeline never ceased to exist, wouldn't that mean that the alternate timeline you created must still exist as well?
Questions like this are pretty much THE reason why time travel makes your head hurt. Time is not a single straight line that goes from point A to point B: It is more like the ultimate tangle of Xmas tree lights, a trillion different lines of lights tossed together without rhyme or reason. Or perhaps, a better comparison would be to a vast ocean, filled with currents going in every possible direction, and nearly impossible to keep track of. Thankfully, this is not, strictly speaking, a story about time travel, or you'd be reaching for your your Asprin right now. Instead, this is a story of an alternate timeline, where a guy named King Sombra, Equestria's perfect asshat, was not stopped right after he escaped from his imprisonment, but instead was able to retake the Crystal Empire, and from there, started metaphorically kicking Equestria in the dick over and over again.
Now, those of you familiar with the Primary Timeline (Or PrimeTime for short), are probably wondering how a single wizard with an army of maybe a thousand ponies, tops, could be such a massive threat. To understand that, I'll need to give you some info on Equestria in general. In PrimeTime, Twilight Sparkle and her friends handled a sizable number of Equestria's problems. Problems, I might add, that would be Celestia's to deal with, if Twilight Sparkle and her friends had not gotten together. See where this is going? Starlight Glimmer monkeyed with the timeline, and suddenly, Celestia's go-to group for solving problems was gone. And things started to snowball from there.
Lacking any other alternative methods due to an absence of Twilight and Friends in this timeline, Celestia had to deal with everything that went wrong in Equestria, and a lot of shit goes wrong in Equestria, every single day. To make things worse, for one thousand years Equestria's entire military strategy during a crisis boiled down to 'keep whatever it is busy until Celestia can come and deal with it'. Up until this point, it worked, because Sombra-level problems were rare. However, let us take a quick look at the highlight reel of all that had happened in Equestria, leading up to Sombrero's escape and invasion.
First off, Celestia's sister, Luna, escaped from the moon. Yes, she was still hopped up on dark magic, and as Nightmare Moon, she tried to overthrow Celestia and steal all her cakes. Celestia took offense to that, as no one messes with her cakes, as the sun princess' massive booty can testify. Two alicorns, equal in power, did battle, and Celestia just barely managed to overcome her sister, and basically sent Luna back to her room to think about what she did for another thousand years.
Second, Discord. Motherfucking Discord. Not that I have anything against the guy personally, but this is someone who can change reality with a literal snap of his fingers. He's the ultimate godmode cheat made flesh. He's in a weight class all his own, and Celestia having to fight this guy in the best of times would be dicey. Worse, this guy showed up not long after Nightmare Moon, so Celestia had barely recovered any of her strength. She had to cheat, and pulled a Discord herself: She tore reality a new space hole and shoved Discord right up into it, just as far as she could. She shoved him so far up her space hole that it would take centuries for him to find his way out, and even then, she made sure to clench it shut, nice and tight, so he'd have a hard time forcing his way out.
Third, a bigass dragon took up residence on the mountain by Ponyville, and began releasing a metric fuckton of smoke into the atmosphere. This blocked out the sun, and made the air difficult to breathe, and would cause a lot of problems in the long run. Celestia tried being nice, but the dragon was kind of a dick, and made disparaging remarks about the size of Celestia's flanks. As anyone who knows anything about females of any species can tell you, this was a spectacularly bad idea. Thus, the dragon had to go. Not having anyone else available who could defeat the creature or convince it to go elsewhere in her stead, she had to go and defeat it herself. She fought the dragon for six days straight before finally suplexing it into a volcano. Seriously, she did that. They even had a stained glass window made to commemorate that event. It looks exactly as insanely awesome as it sounds.
Then, there was the changeling invasion. That was a complete clusterfuck: Security for an important royal wedding was sorely lacking, and Equestria paid the price for it. The bride-to-be, and only other alicorn around, was abducted, and by the time she was found, she'd starved to death in a cave somewhere. The husband-to-be, and leader of the royal guard, was brainwashed, and ultimately his mind was completely destroyed by changeling mind magic: While his body was saved, the cheese had slid completely off his cracker. The queen of the changelings and Celestia did battle as the changeling army invaded the city en-masse. Canterlot was more than half destroyed in the resulting chaos, and while Celestia was able to secure victory through dogged determination, it was a very near thing. The changelings fled the city, carrying their wounded queen with them. Celestia was too exhausted to pursue and try to finish things.
And then Sombra came along, less than a day later. Celestia was exhausted at this point, still recovering from the battles she'd barely won, and was unable to nip that particular evil in the bud. And by the time she was well enough to fly of to the Crystal Empire, Lord Tirek busted out of Tartaraus, and she had to deal with that first, as he was a more immediate threat. Thus, Sombra had plenty of time to retake the Crystal Empire, consolidate his forces, and ready his slave army for war. By the time Celestia defeated Tirek and choke-slammed him back into Tartaraus (Not hyperbole, but sadly, there wasn't time to make a window of this particularly awesome scene), King Sombra and his army of battle slaves were marching into Equestria.
Now, as mentioned, the Equestrian army's battle doctrine consisted of holding actions. This meant that they were great at slowing the enemy's advance, but when it came to actually winning battles, they sucked asses on fire. Had Celestia ingrained into them the idea that they could actually win battles on their own, hell, even just given them the idea that a bit of initiative when the princess wasn't giving them direct orders was a good thing, they might have beaten Sombra's army on the first day. After all, they had a distinct numerical advantage, and while Sombra was a brilliant individual in a lot of ways, he was no expert military strategist. Sadly, Equestria's army leadership was staffed by ponies who were staunch traditionalists, and weren't going to change things just because it was clear standard procedure was failing. Tradition was infallible: Generations of dead ponies can't be wrong, can they?
Sure they can. They had to die somehow, right? Bad traditions do a fantastic job of getting people killed. Sadly, traditionalists make a tradition out of ignoring that fact. 'We've done things the wrong way for generations! You'd insult your ancestors by doing it the right way now!'
Regardless, due to Celestia being extremely exhausted, she could not bring her full might to bear against Sombra when she took the field, even had she been willing to kill a thousand mind controlled civilians to get to him. Instead, it turned into a battle of attrition... and that was exactly what Sombra wanted. Sombra had intentionally timed his escape at a point when he suspected Celestia would be worn out by several rough battles, as various evils were unsealed and ran amok. A full-on, head-to-head battle with Celestia at her full strength would spell instant defeat for Sombra. However, an exhausted Celestia and a war-weary Equestria would be ripe for the taking.
Just like the Equestrians, Sombra's forces didn't fight to kill, but to capture: Every captured pony was outfitted with a brand new brain bucket, and turned against their former allies. Meanwhile, since Sombra's forces consisted mainly of civilians, capturing one of Sombra's soldiers and de-bucketing them did not automatically mean a new soldier for Equestria: Instead, it meant a civilian, often horribly traumatized by what the helmet had forced them to do, and one who needed food, rest, medical attention, and counseling. It meant a new mouth to feed for a country barely getting by during a harsh war that had no end in sight. Equestria got weaker with every defeat AND every victory, while Sombra's forces tended to just keep getting more and more numerous...
Yard by yard, Sombrero The Asshat And The Bucket-Headed Army Of Doom advanced. It took several moons, but finally, the dreaded king marched to the gates of Canterlot itself, an army numbering in the tens of thousands at his back, and confronted Celestia head to head, confident he would be victorious. A mighty battle was fought, and...
...And this is where I happen to come in.
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I awoke with a splitting headache, unable to recall what I'd been doing the night before. Thus, I reasoned that it must be either Saturday or Sunday morning, and Jack Daniels and his buddy Jimmy Bean were holding a no-holds-barred tag-team death match in my skull against Bud Wiser and Johnny Walker. The fact that so many people were inside my head probably explained why it felt like it was going to explode.
Since the searing pain of my hangover would ensure that sleep would be impossible, I decided that the best thing to do right now would be to get the fuck up. The sooner I did that, the sooner I could start searching for something to cure my hangover with... like a Tylenol... or a loaded shotgun.
I rolled off of my back, and got my hands under me... and immediately realized that they felt odd. I couldn't feel my fingers. My eyes snapped open, and I looked down... to see hooves where my hands should be. It took me a few brief seconds to realize that I was no longer a human: I was some kind of horse creature.
What. The. Fuck. What in a million, billion, trillion fucks?