Mass Effect Equus part One: Project Harmony.

by Paradox Theory

Rating: teen
Tags: Alternate Universe, Other, Science Fiction, Adventure, Crossover, Twilight Sparkle, Main 6, Gore, Original Character, My Little Pony: Friendship is Magic
Length: 1583

Twilight Sparkle and her friends agree to help a group known as Cerberus after a strange alien race forces them to abandon Equus.

New.

I suppose that's the first word that pops into my head when I think of this situation.

Here I am, in the Captain's Cabin of a spaceship. My captain's cabin. . .my spaceship. I was made a commander of a ship full of creatures known as humans, who are followers of some cult called "Cerberus".

A man who says he's like "The Illusive Man, but new" asked me and my friends to help him save the galaxy from this threat. He says they came after the reapers. Without these "Relays" to travel the galaxy, Cerberus is stuck in our solar system, and until the relay is fixed we won't be able to leave.

So, new aliens. New ship. New "Illusive Man". New Mission. New Home.

My name is Twilight Sparkle. Commander Twilight Sparkle of the SR2 Harmony. My mission is to find a way to take my home back.

Or die trying.

Note: While this fic may not give as many choices to you, the readers, there will still be choices for you guys to vote on. So please, be sure to read the author notes and vote with your comment.

Published 2017-03-06 09:40:01 UTC
Last updated 2017-03-06 09:40:01 UTC

Prologue: They came from the sky. . .

Captain's Log, Stardate March 19th 9:00 PM 3985

It's cold. This spaceship. I mean, you wouldn't think it's cold from just the temperature. It's at just the right spot.

But there's no life here. Just bland metal, all that protects me from the vacuum of space.

Oh, I suppose, seeing as this is my first space log entry thing. . .(ohmigoshI'mactuallydoingthis,it'ssocool! *An audible smack can be heard, followed by a sharp breath*) Right, I should say my name, for the record. I'm Commander Twilight Sparkle of the SR2 Harmony. I still can't believe that I've become that, and so quickly. I know these logs should be short, but I feel I should record how this all happened. . .back on Equus, when I had a home.

Nine days ago. . .

Twilight came into consciousness as a few worried voices clamored from somewhere near. . .

"What do we do?" A soft and timid voice wimpered.

"What we always do! We kick butt!" A brash voice answered.

"Rainbow Dash, please, try to be civil. We don't even know what they want." A more elegant and beautiful voice chastised the last one.

"Girls, what exactly is the problem?" Twilight asked as she finally sat up, looking at her worried friends.

"Some sort of ~~humans~~ bipeds have landed near town, in the forest." Pinkie explained.

"Hold on, did you say 'land' Pinkie? As in they were flying?" Twilight asked her.

"Yup. They were all flying in huge hunks of ugly looking metal. It was unnatural." Applejack replied.

This had done it. Twilight was curious. With that inquisitive look she was known for, she leaped out of bed and followed her friends out of the building.

As the group walked, they noticed a large cloud of smoke rising from the distance, where Canterlot was.

"I sure hope Canterlot is okay. ." Fluttershy sighed.

"Yeah, it's odd, seeing that much smoke from there. Hopefully the Princesses will get it under control." Rainbow replied.

"Well, as much as we want to help them, we should focus on those bipedal creatures." Rarity reminded them.

"Speaking of which. . ." Twilight spoke up, "What were these creatures like, do they speak? Is it our language, or a different one?"

"Slow down Twilight," Rarity tsked, "We don't know anything about them yet. We haven't seen their faces."

"Wait, what? How do you know that they are bipedal, but you haven't seen a face?" Twilight asked in a confused tone.

"They are covered in more of that metal stuff." Rainbow scoffed. "Let them hide in their shells, I'm Rainbow Dash! I don't ne-" She suddenly froze and looked up at the sky. One by one her friends did the same. More hunks of flying metal approached them.

Then a giant beam of some sort of energy hit Ponyville. That's when a scream cut through Twilight. A scream of pain, followed by several more screams of horror. Then these alien things from the ships landed, and began to attack them.

"Girls, get as many ponies as you can out of here. Head for the everfree, the trees will provide cover." Twilight told her friends, before the group separated and gathered as many ponies as they could.

Twilight had to close her eyes a few times as she ran. Several ponies lay everywhere, bleeding and broken. Most of them had already died, and some were taking their last breath. Twilight choked back sobs as she gathered those that she could find. She sighed in relief as she found Cherrilee and most of the schoolfoals hiding in the school building. With this group, and the ponies she found along the way, she led them deep into the forest.

After a few minutes of running, Twilight and the group ran into a clearing. It was full of more hunks of metal. She noticed they weren't in uniform with the ones that attacked. She hoped the aliens here were kinder. Or at least, she would have been hoping had an electric pulse been fired at her and her group, knocking them unconscious.

Present Day. . .

That was my first encounter with aliens. If you couldn't tell by now, I didn't trust them. It wasn't the warmest of welcomes. What made me angry though, was what they proposed afterwards. These 'humans' as they call themselves are sure strange.

Bipedal, hairless, tall, and covered in metal they call armor. This race was a warrior race. Yet they didn't kill us. I had no idea I'd be made the Commander of a ship. . .

Approx. 6 days ago. . .

Twilight woke in an empty metal room, she didn't like it. It was cold, empty, silent. This room was a husk. She paced for a few moments before calling out.

"Hello? Can anypony hear me?" Twilight called out, the only sound coming back to her was her echo. She continued like this for about an hour by her count before a beep sounded, and some sort of light thing rose from the ground. It seemed to scan her body, before it showed her an image. The image of an alien in a chair. He smiled as she studied him and his surroundings. She took note of his pale skin, dark hair on his head, and his steel grey eyes.

"Welcome Twilight, to Cerberus Vessel SR2 Genesis." He spoke, "You may call me Illusive Man."

"Illusive Man?" Twilight repeated, "That's a strange name."

"It's not my real name. It's more of a title." He replied. "It belonged to another. He died not too long ago, after a man called Shepard saved the galaxy from a major threat."

"Why are you telling me this?" Twilight wondered.

"Because you have a lot of questions, and I'm telling you why I'm here now. You see, this threat left my group badly damaged. I was made the new leader, and our ships were separated from the rest of our race." The Illusive Man explained.

"Was that when you came to my planet?" Twilight asked.

"No. You see, there's these tools we use to navigate the galaxy, some of them were broken. Ours was scratched. We were safe though." The Illusive Man explained before standing and pacing.

"If you were safe, why'd you leave?" Twilight asked.

"Because, those things that attacked your people attacked us. We had no choice but to run and regroup. Our problem was that the tool was damaged enough that it sent us crashing into the planet you inhabited." The Illusive Man sighed. "I deeply regret bringing them to your people."

Twilight sat on the ground as she processed all of this. "Why save me though? Did you save the others?"

"Relax Twilight. I have rescued as many refugees as I could find. They are safe for the time being." The Illusive Man stated.

"How. . .did you know my name?" Twilight questioned, "I never gave it."

"I'll be honest with you. I don't have a lot of options." The Illusive Man sighed, "I had my soldiers ask your people questions. Who your leader is, what you used as defensive measures, and other important stuff. Don't worry, we didn't bring harm to any of them."

Twilight got up and started to pace as well. "I take it you want something from me."

The Illusive Man smiled and turned to face her. "I do, Princess Twilight Sparkle. I want, no, we need your help."

Twilight paused, "What can I do?"

"Your kind are natural diplomats. You can make others feel love and friendship almost effortlessly. If there are other races besides yours and mine, you can help us to barter peace, and stop this threat." The Illusive Man explained.

"So you want me standing around talking to people?" Twilight clarified.

"No. Not exactly. I want you to explore this region of the galaxy. You'll be given a nice map later. This region has somehow been missed by everything in the galaxy, even the reapers." The Illusive Man paused as he took a drink of what Twilight assumed to be water. "I want your help to find anything we can use to help fight our enemies. Not only that, but I want to help you retake your home, and free your friends."

"What?" Twilight gasped, "You mean, some of them didn't make it?"

"It doesn't seem that way." The Illusive Man sighed, "I was told you were part of a group of six. Elements of Harmony, they called you. Three of these elements are still on the planet Equus. I believe their names are Applejack, Fluttershy, and Pinkie Pie. We recovered Rarity and Rainbow Dash. I have asked that they stay with you Twilight."

Twilight choked back a sob. "Okay."

"Okay?" The Illusive Man echoed, "What do you mean by "Okay"?"

"I'll help you," Twilight answered, "I'll help you fight these beings."

The Illusive Man smiled, "Good. I'll send someone to show you around the station. Then later I'll give you the details for what comes next. For now, get some rest Commander Sparkle."

With that, Twilight stared at the blank room. Though she had questions, only one was loud enough to heard.

"Why'd he call me Commander?"

Author's Note

So, what do you guys think of this story? Does it have potential?

Also, after Rainbow Dash and Rarity are reunited with Twilight, I may have her romance one of them. Not sure which. But maybe I'll let you guys choose.