Silly Plan
It was over.
In a final moment of defiance mankind had launched literally all of its nuclear arsenal across the planet, where the barrier had not yet covered, in an attempt to not only destroy themselves, but also destroy the Ponies along with them.
Unfortunately for Humanity, the Ponies behind the barrier were unaffected. Most celebrated the demise of the Humans. However, there were still many Ponies not under some sort of mind control, whom were deeply depressed and swore vengeance for Humanity in quiet whispers.
On Earth, the pink barrier continued to slowly advance over the irradiated wasteland, vaporizing everything Man had made, even the skeleton remains of Humans, it also wiped away the radiation and dust, cleaning the atmosphere and spontaneously causing forests filled with bunny rabbits and rainbows to appear out from nowhere.
All done to ensure that every trace of Humanity's existence was completely wiped away, so that they would be forgotten and be a mere whisper in the eternal silence of an empty void. All the achievements, knowledge, art, literature and everything the Human race had done, were to be disregarded as evil and poisonous to the fabric of society by Celestia's mind controlled Ponies.
Celestia happily trotted into her throne room, this was the greatest day ever, soon she shall spread more joy across the multiverse for Humanity, by ridding them all of their inferior forms to become perfect Ponies. Unfortunately, some shadowy figure of a Human, whose body seemed literally made out of shadows was sitting on her throne.
"What are you doing?! That's my seat!" she shouted.
"Spoken like a true six year old. For a world eating monster, you sure are dumb." said the shadowed being in a deep ghostly voice.
"Who are you?!"
"It really doesn’t matter who I am foolish horse."
In her anger her eyes glowed bright red and her mane became engulfed in flames. The ghost chuckled at her pathetic attempt to scare him.
"You dare mock me! I will find the Elements of Harmony to defeat you demon."
"No, you won't." he laughed maniacally. "I've hidden them in a special place."
"Where?"
"I'm not telling you." Celestia charged at the demon, only to be hit by an invisible barrier that sent her crashing into a wall on the opposite side of the hall. "Now Celestia, there's no need for violence."
"Why are you here?!" she cried.
"Oh, I'm here just to make fun of your plans for multiversal conquest."
"Nothing can stop me!" she shouted as she stood up and stomped her hoof.
"Oh, I suppose you think you have the power to take on the entire multiverse, huh? Even the Combine avoid certain universes."
"I will bring harmony to all of Humanity."
"Tell me, how does wiping out an entire species bring them harmony?"
"Because we are better than Humans, that's how!" she roared.
"Oh right, how could I have forgotten. Ponies are after all perfect master race." he said sarcastically. "Personally, I think Humans are better, but that's just my opinion."
"But my Ponies and me destroyed them!"
"Using cheat codes like invincibility, hiding behind an unstoppable wall of death and turning their own into zombies. If you had actually fought the war in the Human saying 'man to man' without cheating, you would have lost the war in about two minutes."
"But Humans would win then."
"Ah, so you do realize Humanity would have kicked your royal butt, if you weren't a hacker."
"Hacker, what's that?"
"I'm not going to explain what that is. You should know though, I had offered a Human the power to defeat you. Surprisingly, the Human had rejected my offer."
"Why?"
"Because that person did not want to become something like you and wanted to die with integrity." she said nothing in response. "Can I ask you a personal question?"
"What?!" she shouted defensively.
"How did it feel to kill your sister Luna and once fateful student Twilight Sparkle?"
"I-I.... I.... ..I.... they were corrupted by Humanity's influence and tried to stop me from saving Humanity, I had no choice." a few tears ran down her face as she spoke in a low voice.
"I wonder, does it hurt you to know that Ponies and Human are actually friends and lovers in some universes?"
"That's impossible!" she shouted.
"You yourself in some universes do have a Human as a partner."
"You lie! That's all impossible!" she screamed.
"I hope this gives you some deal of closure before the end comes."
"What do you mean?" she said curiously.
"I have alerted some Gods devoted to the protection of Humanity across the multiverse to what you did in this universe. Saying they are upset would be a little bit of an understatement."
There was a crash, followed by the door of the throne room being sent flying across the room. The ghost summoned popcorn to watch as hundreds of large angry magical beings, giant cyborgs and even other alternate Celestias stormed in to surround Celestia of this universe.
"Goodbye Celestia, it was nice knowing you."
And then the magical beings, cyborgs and alternate Celestias tore Celestia to pieces.
Once Celestia was dead the magical beings had left and all the Ponies that were under her mind control had stopped celebrating the demise of Humanity. The Newfoals however became little more than vegetables in the mind, without a leader they just mostly stood there doing nothing and starved to death.
It took time, but after a few years Ponykind was able to turn enough Newfoals back Human to just about have a viable population. Unfortunately most had died during the process or became savagely violent on a similar same level to that of a cannibalic zombie, whom had to put down. Luckily, they still had just enough Humans that were sane and could carry on the species.
Humanity's lived again, all be it far weaker than before, but with help from good Ponies, the Human race could regain it's former glory even faster than before.
The End