//------------------------------//
// Prologue 
// Story: The War 
// by runforever101 
//------------------------------//

A lavender unicorn raced through her decimated town. Buildings were burning, falling, and nothing was left for some. The sky was completely black with a red wormhole in the middle. Despite all of these things, only one thing scared her, a message written in fire on town hall. “Your Princess’s are dead. We are your new leaders, slaves.”
Twilight tried to dodge the falling balls of acid as she continued to race through town. Encased in her magic was a small colt. His mane was navy blue and his coat was azure. “Mommy?” he whimpered, as his horn flickered a little, light blue magic bursting from the tip.
“Moon Sparkle, you will be just fine.” She stopped for a moment and looked for a building, a special building. Among the apocalyptic setting, she was able to find a small, metal outhouse.
Twilight Sparkle raced towards the building. Her heart felt like it would fall out of her chest and her hooves burned from all of the running, but she had to make it. She had to.
As she came up to the entrance, she flipped up a box and pressed her hoof to it. Her forehead was full of sweat.  Go faster!They’ll find us!”
As soon as the door unlocked for the unicorns to enter, a cold voice spoke. “Stay right where you are.”
Twilight slowly turned around as she set her son down behind her, facing the door. “Go inside,” she whispered.
“Black Ink!”
“Twilight Sparkle.”
Moon didn’t know what to do, he could go inside and leave his mother to die in the hooves of those monsters, he could stay outside and die along with her, or he could drag her inside as well.
He tried to use his magic to drag her in too, but she closed the door behind him. “No! Mommy!”
Twilight tried to stare eye to eye with the beasts. They looked like ponies but had completely red eyes and pointy teeth that could be extended. They could also get rid of their grotesque features to look exactly like ponies.
“It’s been a long time since we last saw my dear. Manehatten, 1010. We met in a bar; I was merely a scout for my planet then. We fell in love and dated. One night we even went to your apartment. When I tried to tell you who I really was you tried to kill me. That hurt, Twi. And Moon Sparkle is my son, but you still hate me!”
Twilight tried to look away, despite the way he looked in his true form, he was still handsome. He had a short wavy mane and tail and a smile that would make you smile too.
“Moon Sparkle may have your genes, but he is not your son! He is Moon Trust’s son and always will be.” Twilight growled.
The stallion tried to look away. He always remembered one thing after that night. Don’t let her see you cry.
He furrowed his brow and pulled Twilight in. He felt his lips touch hers. Same as always he remembered. Never chapped, tasted like cherries, and the most amazing feeling he ever felt. It was all so amazing until she slapped him with her hoof. “I hate you!” She growled, as her horn lit up. Some of the the aliens did too, but he turned around. “Let her go.”
Twilight ran in while she had the chance.
“She’ll be back.”
..............................................................
Twilight ran into the hut to be greeted by an elevator. She stepped in and let it do the rest. Soon the unicorn was downstairs with a large group of ponies. 
She raced through the crowd to get to a room in the back of the shelter. “Moon, go find Big Macintosh!” Twilight whispered to her son. “I’ll be back in a second.”
The unicorn entered the room, finding the Elements of Harmony, her brother, and Cadence. “Hello Twilight,” she said gravely. Bags hung from the bottom of her eye like they had in the Crystal Empire. 
“Cadence..” Twilight tried to hold back tears. “They say they killed Princess Celestia and Luna!”
She ran over into the young alicorn’s comforting hooves. “Don’t worry, they are strong. I am sure they are alive.” I hope.
“Right now we need to find a way to get rid of the threat, so we have brought you girls here to summon the Elements of Harmony. Auntie T said she knew a threat was coming just weeks ago, and built this secret hide out. As you all know, when the meteorite crashed, the sky turned red and those evil ponies poured out. My aunts tried to stop them but we haven’t heard from them since. Twilight, if you remember the meteorite shower many years ago, one of them held the pod that… He was in.”
Twilight lowered her head as cadence continued. “The Element necklaces have been relocated to here, and I have them right now.”
The pink mare pulled out a briefcase. She slowly opened it with her magic and handed it out to each of the girls. “Princess, we all have children and Ah’m pregnant… What if we don’t make it?” Applejack asked, worry in her eyes. 
“You won’t. But if you do for some weird reason, your children will go to siblings or other members of your family.”
“But I’m an orphan, Scootaloo and Sweetie Belle are dead, and Pinkie’s family disowned her.” Rainbow Dash interjected. 
”We will find good homes,” Cadence said merely. “But for now, our only chance of survival is you.”
“We’ll do it Princess!” smiled Twilight
While rainbow wasn’t to happy about this, she nodded along with the rest of the ponies.
“Good. Now go. The fate of Equestria rests squarely in your hooves.”
……………………………………………………………
Everything happened too fast. The Mane Six ran out with their necklaces and crowns on and got into formation. Before the spell could be performed, the aliens attacked. They took down Applejack first, seeing that she was the least able to fight back, being pregnant and all. A female one stood on top of her and ripped out her throat.
Next was Pinkie, then Dash, and Fluttershy was beaten to death rather than having her throat ripped out. Rarity put up a pretty good fight, throwing up her hooves and beating anyone who dare come near the fashionista. After awhile, she stood completely still and fell to the ground. A bullet had gone through the Element of generosity. Twilight laid on the ground as she coughed up blood and let tears stream down her face. Her eyesight was blurry, but as her friend’s shooter came closer, she noticied who it was in a heartbeat. “Black..” She couldn’t finish her sentence. His eyes were also filled with tears as he lifted a gun. “I’m sorry my love.” Then everything went black.
…………………………………………………………………………………
Many, many years later the little underground habitat became a village, a town even, and Ponyville became a battleground. Moon Sparkle grew up to become the first leader, and his son became leader too. Each one kept a secret passed on by their father’s.Never tell anypony who you really are.