Star Trek Equestria: The Fall of Harmony

by NightmareTRXY32

Rating: everyone
Tags: Twilight Sparkle, My Little Pony: Friendship is Magic, Dark, Alternate Universe, Human, Main 6, Other, Science Fiction, Crossover
Length: 2190

Twilight Sparkle and her friends had always been there to protect Equestria from outside Dangers. BUt about from within? That pales in comparison to the chance to go to Space. But what happens when they discover the wreck of an abandoned starship?

Twilight and her friends have been through many encounters, and faced alot of enemies, but this maybe something that she has have never seen before. On their first interstellar mission on Equetria's first starship Twilight discovers there are some terrors that will freeze your soul. They encounter a ravaged ship with a dying crew member. This is the story of the events leading up to their encounter told through various other characters.
Twilight also realizes that she just might of made her home a target for conquest. and all of this after getting a chilling transmission back from her homeworld.

Published 2016-07-09 12:30:01 UTC
Last updated 2016-08-28 06:19:31 UTC

A Chance Encouter

They would be the first ponies to set hoof into space. Those were the words the Princess told her friend and former student Twilight Sparkle as they walked through the halls of Canterlot. The princess had been very specific when it came to those who would man Equestria's first warp capable starship. The vastness of space had always caught Twilight's curiosity multiple times before, but now she'd be the first one of her kind to explore its mysteries and wonders first hoof. That and her friends would be there to aid her in her Journey. And not only that, she'd also be the captain of this intergalactic wonder that was towering in front of her. The hall they had been in lead them both to the causeway that would serve as the catwalk to their new space craft.

The name of it was something that Twilight had read about in an ancient tome on Unicorn Magic years before her ascension to Princess hood. Celestia had christened the vessel Absentia, which means lost, in one of the Oldest unicorn dialects ever recorded. Twilight could feel the excitement and anticipation build within herself as she kept staring at this Metallic marvel. It had been designed to have a crew capacity of 100 but could be operated by less than 20. Among those elected for the crew were Derpy hooves, her friends from Canterlot Minuette, Lyra, Moondancer, and Lemon Hearts. Her friends from Ponyville were selected as well as Doctor Whooves. IT seemed that Celestia had been aware of his expertise in operating advanced mechanical equipment. She had learned from a valued source that he wasn't even really a pony. He had come into this form when he was near death and his regeneration was interrupted and pulled part of him into their corner of the space time continuum. So theoretically he was now in 2 places at different times.

When the princess confronted him about it, he asked that she not reveal any of this to Derpy. Apparently spending time with the ditzy mailmare had reminded him of Rose Tyler from where he been before ending up in Equestria. For one split moment in the annals of a Timelord, he had found that he had fallen in love with the human. Seeing Derpy reminded him so much of her. Her smile, her positive, and bubbly, attitude to life in general. And last but not least, her unyielding love for him in the end. Celestia had promised him that she wouldn't divulge any of it.

IT had been 5 months since the launch of their starhip, and Twilight was still eager to see what it held in store for them all as she had been on the day Celestia had first revealed its presence to her. Most of the equipment on board had been designed and tested for science and planetary exploration. But it did have formidable weapons designed around Alicorn magic. Twilight knew, she had designed both the exploratory aspects and offensive aspects of the ship prior to launch. Apparently Celestia had taken her research into account and decided the best pony for a project of this nature was Twilight herself. About a parsec away from Equestrian space came their first test of the sensor array. It detected a metallic mass about the size of their craft. As the Absentia approached the coordinates Twilight turned on the View-screen on the Bridge to get a glimpse of what lay out there.

The craft in front of them was blasted with scorch marks, Twilight assumed they looked like the kind of blast marks that could be left behind by extreme heat. She had seen something like this before back on Equestria. The kind of heat marks left by strong levels of Fire magic. As soon as they were within teleportation range, her Minuette and 2 other unicorns put on Space suits and helmets, and transported themselves over to investigate. What they found was amazing, and grim all the same. Apparently from the looks of it, this ship had been attacked and boarded by the looks of it. There were a few bodies here and there on what was once the bridge of the vessel. Twilight and the others walked around to investigate the rest of the ship before heading back to exploration mission. Twilight found what was left of the main computer in the Engineering section of the ship. She also found several more bodies. The crew of this ship were bipedal in nature, similar to the humans she came across when she went after Sunset Shimmer through use of the Magic Mirror. Then something caught her attention, one of the bodeis were moving, somewhat.

" What are you doing," It asked Twilight.

"Please dont be scared, we found your ship like this, and we came to investigate,"She answered back.

"Your.. Your quadripeds?", The alien asked hesitantly.

"Yes, i take it you've seen one before?" Twilight had about a thousand things she wanted to ask it, but from scars all over its body, she realized it was breathing its last.

"Yes, but not this far out. My name is Krang, of the Klingon Defense Force." He spoke those words with what pride he could muster in his current predicament.

"What happened to your crew, Krang?" She spoke softly, " Your the only that seems to be left nearly alive."

"We were attacked by an enemy of our Empire, and that of our allies." He said in between coughs of blood," They are called the Borg."

The Borg were a race of half organic half cybernetic beings whose only purpose was to assimilate others into their collective for what they called perfection. Apparently the planet Twilight lived on border the space just outside of the Alpha Quadrant. And she also came to the cold realization that she might of just made her home a target for these 'Borg'. Before he died Krang imparted his memories to her. Apparently one of his ancestors had been married to something called a Vulcan, and it enabled him to perform a mind meld with Twilight.

Many years ago, before the meeting of Twilight Sparkle and Krang

Stardate 543. 2418

The Klingon Romulan Border.

USS Deavers Patrol Route

"Captain, we are approaching the Klingon Romulan border," Ensign Davis told his commanding officer, Captain Jennifer Laughlin.

"Prepare to open hailing frequencies," She had been order to this area by word of StarFleet command, She was to rendezvous with a Klingon bird of prey and commence annual readiness drills. They were then to reported their readiness status straight to the High Council, as well as Starfleet.

"Captain," Ensign Davis reported," we have 2 Romulan Warhips decloaking off our Starboard bow."

That was odd, what are the Romulans doing in Klingon space? She had her operations officer attempt to contact the ships and request information on their intentions. The hails they sent to the Romulans went largely unanswered. Then the Romulans responded, by firing disruptor blasts at them.

"Sir, they firing their forward disruptors," ensign Davis yelled as he was nearly tossed from his chair at the helm.

"Raise Shields!", The captain bellowed to the Operations officer. The Warbirds fired on the Deavers with a volley of plasma Torpedoes before resuming the disruptor fire. Her ship had survived combat during the Dominion war, Romulan disruptors were nothing compared to Jem H'dar weaponry. This time was a bit different. Apparently these Romulan ships had upgraded their weaponry from captured Borg Technology. But the Deavers shields still held under the pressure.

"Send a message to Starfleet and advise Admirals Heartway and Janeway of the situation," the transmission was sent out, but she didn't know if they Romulans were jamming the frequencies or not. She could only stand on her bridge and pray that the cavalry would show up if Starfleet got the message at all.

Chance Encounter pt2

Krang was gone, his body limp in Twilight's hooves. She could only look down at his now cold body and wonder if there was something she could of done to save him, to try and heal his wounds. But she came to the conclusion that there was nothing she could of done except be there for him in those last moments. She hated it, that death was so finite, and that there was no way to prevent its occurrence.

The memories were still fresh in her mind as she continued to stand there in front of Krang's body. The Klingon had passed on some time ago, but left her not only his memories, but one last gift. He imprinted a telepathic thought into Twilight that brought a soft smile to her face. She smiled as she could see him stand before her and kiss her on the forehead, and thanked her for finding him in his last moments and still leaving him with at least one happy thought before dying. She told him back telepathically it was the least she could do, and she was happy to have been there for him.

On the outskirts of Equestrian space The Absentia came across another derelict ship after Twilight and the away team beamed back from the Klingon wreck. This one was different, but it strangely matched a design she had seen Celestia show her once when the Absentia was first being designed and its future systems tested in the Canterlot Equestrian Space Labs. SHe remembered Celestia describing a meeting of humans several hundred years ago during her early years of ruling Equestria. These humans had come in an interstellar ship called the NX-02 Columbia, Captained by one Rachel Ramierez. They had traveled to this part of the galaxy through a subspace corridor that had been discovered some time ago. The ship on the Absentia's sensors matched the configuration to a T. Had this ship been adrift in the vacuum of space all this time?

The only to find out was to try and board her. When they boarded the ship, lifesupport was offline, and there were bodies still manning their posts. It looked as if the vacuum of space had preserved them in perfect condition. Twilight activated her suits gravity boots and walked over to the nearest console. The device she had with her would let her access their systems to determine just how long the ship had been out here and how long the crew had been dead.

The last remnants of the crews voices could be heard as she played back one of the audio logs. She went pale as she heard people screaming and sounds of phaser fire. She looked up to see the others were worried she had heard something horrible so Twilight decided to play it out over the ships nearest console.

Flashback- NX 02 Columbia-

"Captain Ramirez to the bridge, we've detected a mysterious ship on Sensors and its not answering any of our hails". The helsmman said over the ships intercom. The NX 02 Columbia had come across a distress call from a cargo ship that did regular trade runs to the Terran system. The only words that could be made out were, " under attack... Metal Cube.. Systems failing." That was it as far as the distress call said.

"Let's get over there," Captain Ramirez told her crew, they were the second-best ship in the fleet compared to the Enterprise, Columbia's sister ship. As soon as they got there the ship was being attacked by a large Cube-shaped vessel. As soon she saw that, something that Johnathan had told her years came to the forefront of her mind. It was about Cochrane's first warp flight and that the images that been taken by the Phoenix. Images that even now still existed in a Starfleet database were filed under Classified by Starfleet Security.

One of the images had shown a large black metal Cube with integrated lattices on the outside of its hull. It had been described that this " race" of cybernetic beings had come to assimilate earth in the past, thus changing the outcome of history. From his own description, he had stated the sight of terrified him to no end.

Once the cube detected Columbia, they received a hail," Columbia, Registry number NX 02 , secondary unit to the Starship Enterprise, you will be assimilated, Resistance is Futile." The Cube began probing Columbia's defenses and once locked on , engaged their tractor beam. The Columbia opened fire, taking out the tractor emitters before the Cube adapted.

"We've been boarded, Section 32 C Deck,"The helmsman turned to the captain, the fear in his voice was evident. This was the same tactic they had used on the Enterprise. Disable the ship's power grid before eventually assimilating the rest of it. She ordered that they keep firing to try and distract the Cube further. It didn't work as she had hoped. The Cube fired several torpedoes that took out the engines, leaving the ship adrift in space.

Once the Cube had determined that Columbia was no longer a threat, it entered what appeared to be a green warp conduit before disappearing off of sensors.