Chapter One
Twilight's first thoughts when she came to were something along these lines: WHERE THE BUCK AM I!? She would have liked to have spoken this, but she was suspended in a green fluid with various tubes going into her mouth and down her throat. Before she was given a chance to panic, she took notice of the room she was in. From what she could tell, the room was entirely made of metal, with many lights and various sounds, all muffled by whatever fluid she was in.
Continuing her look around the room, Twilight noticed a creature in front of what looked like a glowing window. It was, from what she could tell, bipedal with next to no hair, aside from on the top of its head, which was a rat's nest. It was wearing a lab coat that went down to its legs and wore black shoes. After a minute, it looked up, seemed to get excited, and left the room through a couple of sliding doors.
When it had left was when Twilight began to panic. Oh sweet Celestia, where am I? How did I get here? What in Equestria was that thing? She would have mused further were it not for the creature coming back, with another one with it. The new creature looked much older than the first one. It had a simple shirt on with jeans and a vest with many bulging pockets. The two were talking. It was slightly muffled, but somehow she could still understand them.
"Are you sure?" the new one asked in a gravely voice that she deemed to be male.
"Positive. It definitely isn't Protoss and there aren't any traces of Zerg in its DNA, though its DNA did find a partial match in the data systems." the first replied, also male, but much higher. "It seems to match with an old genus of equines, though with several differences." He motioned to the top of her head. "We can't tell what it's used for, but it's clearly a horn."
"And what's that other thing on top of its head?" the second asked.
"That we don't know." the first one replied, looking kind of sheepish. "We couldn't remove it and whenever we scan it the devices start to go haywire."
At this point, Twilight began to struggle. She tried using her magic to break free, but she had not enough energy. The two noticed this and watched as Twilight positioned her forehooves on the glass and, using all the strength she could muster, bucked the other side of the tube she was in. The tube then shattered, green fluid flowing everywhere and left Twilight on the floor with several cuts and scrapes on her legs from the broken glass.
The two creatures backed off, the older one standing in front of the younger with a black device pulled out and pointed right at Twilight. Twilight, coughing and spluttering, made a mental note: Never let that stuff get into my mouth again. Ever. After a few moments of that, Twilight pulled herself up and got a good look at the two creatures.
They both had pale, pink skin, almost cream colored, but that was where the similarities ended. The first one had slightly reddish hair and it was very untidy. His face seemed young and full of excitement. The other's hair was sleek and black, though with some grey in it to show his years. His face was much more weathered and had some facial hair in the form of a beard. He seemed to have a sense of suspicion about him.
After a few minute of the three of them staring at each other, the one in the lab coat stood in front of the other, blocking Twilight's view of the device. "Sir, I can't let you shoot it. Who knows what it could do for our research!? We don't even know if it's hostile!"
"But what if it is? It just smashed through your stasis cell, Stetman. How do we know it won't try to attack us?" the other replied.
"I have a name and gender, you know." Twilight said indignantly. "And I would never hurt anypony unless they were hurting me or my friends."
The two looked shocked at hearing Twilight speak, seemingly reeling from the fact that they had kept a fully sentient being in a stasis cell. The one who's name seemed to be Stetman spoke up.
"You can talk?"
"Of course I can!" Twilight replied angrily. "My name is Twilight Sparkle and I demand to know where I am this instant!"
The older one stepped forward. "My apologies, Ms Sparkle. We didn't know that you were.. well.. sentient." he said apologetically. "Allow me to introduce myself: I'm Jim Raynor, commander of this fine vessel known as the Hyperion. This man here is Egon Stetman, lead scientific researcher on board. We are currently making our way from the planet Char. If you don't mind me asking, where are you from?"
Twilight hid her confusion from Raynor and Stetman about where they were and decided to answer Jim's question. "I'm from Equestria." she said. "It's ruled by Princesses... Celestia... and..." That's when the realization hit her: Where are my friends?
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Somewhere within the Hyperion...
Some of the crew members within the Hyperion thought they were hearing things throughout the day. For some, it was high-pitched laughter, for others it was hushed voices. Several shrugged it off, but it spooked several others. It wasn't until later that they heard a message go through the PA system. A message in a voice they all recognized as Raynor's.
"Attention all crew members, I have been informed by a recent... addition to our group that there are several, well, ponies on board the ship. They are..." they all heard some ruffling of papers, " ah. There are five of them. An orange one who answers to Applejack, a blue one who answers to Rainbow Dash, a yellow one who answers to Fluttershy, a white one who answers to Rarity, and a pink one who answers to Pinkie Pie. Keep in mind, not only are these five sentient, they are also probably very scared. Do not give them reason to fear you. Just lead them to the bridge of the Hyperion.
"Now, this message goes to the ponies in question. Your friend Twilight is here, and she wants me to let you know that she's waiting on the bridge for you as well. Just try to find a crew member and have them lead you to the bridge. I give you my word as the commander of this vessel that no harm will come to you. That is all."