Prologue: How it all fell apart in Equestria.
"So, we're sure inter-dimensional travel will work, right" said the worry wart of the three equine scientists, "I mean if it doesn't work, something might happen to Equestria and-"
She was interrupted by one of the other scientists "hey everything's going to be fine, besides it's not like us to try something and give up before the last test, and no matter what happens we can still teleport into another dimension using lots of unicorn magic."
The mare calmed down and said, "I know, but it's just that I'm nervous to see what will walk in when we open the portal to another dimension."
The other scientist who remained quiet turned from his work and nodded to worrying mare, "yeah, you may be right, but if we don't try, surely we'll never succeed in finding out if there is only our world and nothing else to find other than open space."
The mare relaxed and let out a deep breath and returned to uploading the data into the portal and calmly said "I guess you're right, our curious mind will eventually get us to work on this again Doctor," She then turned and fluttered her wings while typing "still I hope to find something other than a human, that time in the high school is not something I wish to go to again."
The Doctor chuckled and said "I agree Twilight, but that was only one universe; it may be very different if we find some other human universe full of different humans that are a lot like you and I in personality."
The third scientist rubbed his head with hooves and said "you sure you aren't a professor Doctor, because my professor always made my head hurt about facts that he made about anything," he shook his head to clear his headache, "can't you just speak normally and not make it so hard to understand what you're trying to say?"
The scientists continued their work with the occasional talk before the next step, and cue time skipping music (if there is any). The Doctor went up to the control panel and flipped the switch to turn the machine on. The results came… slowly, but eventually a human walked in through the portal and looked around as if confounded by the room and every equine. Soon enough the man turned to the alicorn and asked "where am I?"
"You're in Equestria my friend, you were teleported here by a portal that we created to cross into other universes," the human looked even more confused by the mention of where he was than how he got there, and without warning more humans came in through the portal and looked as confounded as the first one. This took about an hour for Twilight to tell every single human what was going on and why they were here.
They stayed in this universe, surprisingly, Twilight wrote in her journal, and they have offered to take positions as workers in the Equestrian economy and even ask to be a guard every once in a while. Eventually a lot of the humans did join either the Equestrian army or became a royal guard, but trusting our kind with that kind of role is foolish. A large amount of human soldiers and guards took the guns from the armory and murdered Princess Celestia (with lots of bullets and lots of people to throw them at the Princess), but as soon as Twilight and Luna noticed them waging war they sent for the army to come and assist the royal guards. It took the army about an hour to get the humans to retreat out of Canterlot (no surprise right?), and they had to evacuate every pony to a safe zone where they couldn't get hurt. The humans were taking towns without ponies in them and made them fortresses and make frequent attacks on the safe zones, but fortunately for every pony there were the elements of friendship to come and lead small militias to defend the safe zones, but both sides are getting weaker every day and need more help.
"Perhaps a certain wanderer of universes will come and save the day," said a dark figure known simply as Death, "you should go fix the balance, Wanderer."
There is a teenage boy in the corner of the white room wearing a black hoodie and black jeans. He has a backpack with a sniper rifle attached to it, and nine millimeter pistol equipped to his person, but has a long strand of hair hiding the left side of his face. He smiles and says "I guess I should, it doesn't look like they're going to get out of that mess by themselves without some extra help." He quickly looks toward the now open portal to the Equestrian universe "after all this place does get quite boring when it's just a void. He goes towards the portal and waves goodbye to Death.
Now the real story begins… in the next chapter!