As Changeling and Pony blood mingled on the ground, Scott stood above a Changeling corpse with a hole in its chest, courtesy of his laser weapon. He was heavily injured, near the point of passing out, but it was almost over. The battle was winding down, and there were only a few Changelings left, but most of the Ponies that were trapped were being finished off by the remaining ones. Luckily, most were being saved by Royal Guards. Suddenly, Chrysalis called for a negotiation outside Ponyville. With only a dozen renegade Changelings left, it was clear who was going to be surrendering. Right?
"Surrender, foals!" shouted Chrysalis. "I have a power you cannot even hope to attain!"
"What would that be?" Celestia asked calmly.
"Power to destroy the universe!" claimed Chrysalis. "I read the human's mind during the night, and created a spell that can function as the Supernova Device!"
Celestia smirked. "I doubt it."
"I shall prove it!" Chrysalis roared, livid. Her horn lit brightly, and the sun above began to spark, grow red, and expand. Sweat ran down Chrysalis's cheek, and Celestia's face was a picture of shock for a moment, before she began writhing on the ground.
"Our Sun has became tied to my life force." she whimpered as tears ran down her face.
Everypony stared at the sky in shock as the sun seemed ready to burst. Suddenly, a shot rang out through the day, and Chrysalis stared down in surprise at the smoking hole in her body. Her magic stopped, and she slumped over, dead.
"I'm afraid I can't let you do that." stated Scott as he unsteadily walked closer to her body. Nopony moved. He grinned like a madman, before colapsing in a heap, barely breathing.
"He's still alive!" shouted Celestia. "Medic!"
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Scott heard a steady beeping noise as he woke up. When he opened his eyes, he saw the Elements standing over him, anxious looks on their faces.
"Miss me?" he asked with a grin.
"Don't do that!" Twilight frowned. "You were in a coma for a week!"
"And I have an appetite to match it."
Twilight sighed. "You're being released tomorrow."
Scott's eyes were wide with shock. "So soon?"
"Now that you're concious, we can safely perform healing magic on you. Your lessons on anatomy helped me create healing spells that should help heal you. Theoretically." The last word was mumbled.
Scott had a nervous look on his face. It was time for magical healing. "Will... Will I feel anything?" he whimpered, sounding like a foal.
"No." Nurse Redheart answered. "You'll be anesthetized."
Scott looked uncertain, but before he could ask a question Redheart continued. "Yes, we adapted an anesthetic specifically for humans."
Satisfied, Scott closed his eyes. When he opened them again, Twilight was there, ready to take him home. In the next few days, there was a celebration, featuring a special award for Scott for defeating Chrysalis. This was accompanied by a Royal Pardon, for the near-extinciton of Humankind. By this time, his friends at the spacecraft had created a small village, and were opening to trade with both Ponies and Changelings. Scott left the library, and went to live in a house created for him, right next to the spaceship. The Changelings had worked out an alliance with Equestria, resulting in trade licenses and a few citizenships. Many Changelings went on to be famous movie stars and actors, as well as the occasional Changeling in another career. One day, as he watched the sun set, Scott saw something in the sky. It looked like a meteor, but it didn't seem to be burning up...
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The spacecraft landed near Scott's, and the Elements and Scott were standing there, waiting for it to open. When it finally opened, Scott's jaw dropped in shock. "Richard..." He whispered.
Richard stared with a grin. "I should have known. You're the one who did it, started the Apocalypse. Am I right?"
"But... But..." Scott spluttered. "How did you survive?"
"I had my Bubble. We were sent to destroy it all. I was going to countermand the order, and go on strike. I never guessed. Your act was quite convincing."
"You were going to go on strike?! Why didn't you tell me?!"
"I thought you were with them. I couldn't risk it."
"Same for me. You never seemed to raise any objections. Same reason as me. Huh." he broke down sobbing.
Richard frowned. "I would have done the same in your place. It's fine. Humanity will go on, with a new beginning. I forgive you."
The ponies watched in confusion. Without a translator, this "Richard" didn't even seem like an intelligent life form!
"And here's the local indigenous population." Scott turned and pointed. Noticing their confused expressions, he realized what was wrong. "Oops." he blushed. "You need a translator."
Richard laughed.
After introductions went around, and these humans were moved into the growing village jokingly called "Humanville", an official alliance was made between all humans and the ponies. Equestria seemed a little crowded, after two more species were added to it. The next step? A space program.
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Twenty years later, a spacecraft was being sent up. This was no ordinary spacecraft, it was a colony ship. Sent to colonize a nearby planet, its population was equal part Pony, Changeling and Human. Earth Ponies could farm, Pegasi could control the weather, and Unicorns could do various other tasks at the colony. Changelings, who could change their biology at will, would be useful in setting up the colony before the ecosystem was regulated. They also made great guards. Humans could invent, and complete tasks with magic-sensitive equipment, and use items that required opposable thumbs. As Scott watched the ship blast off, Twilight by his side, he smiled and saw amazing things in the future. With an alliance this strong, soon the whole universe would be at their fingertips.