Star Trek: Friendship Among the Stars

by Twi-Fi

Rating: teen
Tags: Alternate Universe, Human, Other, Original Character, Star Trek, Spike, Science Fiction, Cutie Mark Crusaders, Crossover, Main 6, My Little Pony: Friendship is Magic
Length: 9058

Join the first all-pony crew in Starfleet as they explore the galaxy, make friends, and defend the Federation from a dangerous political faction.

When the HMS Equestria sets out on her maiden voyage, they're doing nothing more than charting nebulae is search for different forms of life. Officially, that's all they're doing. But, behind sealed doors in a dark room, select crew members are part of a clandestine investigation of a growing faction within the Federation.

Published 2016-08-04 20:10:01 UTC
Last updated 2016-08-04 20:10:01 UTC

Charting New Territory: Part One

Captain’s log, stardate 42286.3.

Our mission is to explore the Lambda 023 sector of the Alpha quadrant—an unexplored remote region of space just three parsecs from the Beta Quadrant. This is the maiden voyage of the H.M.S. Equestria with an all-pony crew—a landmark day for the Federation. And due to not many ponies being in Starfleet, I weighed in a great deal on the selection of my senior staff. We have a great crew, ready to meet the challenges that lie ahead.

The first leg of our journey will be to take us to the starbase 287 to pick up additional crewmembers and provisions before embarking on our mission of exploration. The ship will be ready to get underway in a few hours, and I’m curious to see if these galaxy class starships are all they’re hyped up to be.

Applejack closed her computer and sat back in her chair. Her ready room had been decorated with pictures of her family and farm. The wall behind her was painted mute-green with golden apples, and the wall to her right hung a wooden case, displaying her medals and awards. The other wall had a holo-image of her pinning ceremony with Admiral Torres. The caption below read: ‘Stardate 42253.06, CAPT Applejack pinning ceremony: The first officer of Equus to earn the rank of captain. May her ship always bring her home.’

Tired of poring over the mission briefings and status reports, Applejack spun in her chair, fixing her gaze out her window. But instead of the comforting twinkling of distant stars, she was greeted with the view of gantries, heavy shuttlecraft traffic, and the stark interior of spacedock. However, the constant back and forth of shuttlecraft captivated her.

In the window, she saw her faded reflection staring back at her. The four pips on her collar were still a refreshing sight. The novelty hadn’t quite worn off. The eye-catching red uniform fit snugly around her barrel, leaving her cutie mark on display. The old uniforms never fit right; she was more than excited when Starfleet finally let a pony design them and even happier when they omitted pants and allowed cutie marks. If only hats were in regs…

The comm system beeped. “Captain. Bridge.”

Applejack shook her head and spun around to tap the comm panel. “Applejack here, go ahead.”

“Captain, Ensign Harvest reporting all provisions and cargo are aboard.”

“Very good, Ensign. Secure port and starboard watches. Have all departments muster with their divisional officers and prepare to get underway. I want all senior staff in the conference room in fifteen minutes.”

“Acknowledged, Captain.”

“Well, I reckon I handled that pretty well,” she said to herself as she collected her mane, bunching it all together, she tied it near the end. “I’m just an executive officer who gets the final say.” She smiled, remembering her first FITREP. Her CO had given her mediocre scores and called her a ‘stubborn mule.’ In response, Applejack filed a grievance nearly starting a legal proceeding.

She was determined to prove she was a more capable officer and offended by his report, but ultimately she proved his point: she was stubborn. Years later he apologized for his insulting remarks, explaining he always admired her determination and honesty, she just needed an ‘attitude adjustment.’ Back then he was Captain Torres; now at Admiral, he was more than happy to pin captain on her collar and shake her hoof.

Looking back at that young and stubborn ensign who was going to ‘reshape Starfleet,’ bad FITREP in one hoof and personal grievance in the other, Applejack wondered how she made it all the way to captain stirring up the ruckus she did. But there she was, sitting in her ready room on her ship, preparing to take her first steps into the unknown.

No matter what any of the experienced captains say about ‘being fully prepared when you get there,’ she couldn’t think of a time when she felt less prepared. Serving as an executive officer meant she had command of the ship sometimes, but the captain usually set the agenda and orders to follow before leaving her in command.

All trepidation aside, Applejack liked the idea of finally being able to run a ship the way she saw fit.

About time I get to it.

Applejack crossed her ready room and stepped onto the bridge. Ponies worked intently on their consoles as they prepared for departure. Starfleet crewmen were going over checklists and last minute installs. An engineering team sorted a small pile of isolinear chips on the deckplate. Each chip was inspected and slid into the open panel at the engineering station.

“Engineering, transfer power to the secondary sensor array, the primary system is taking too much power.”

“There appears to be a faulty relay, the primary system shouldn’t be drawing that much power from the secondary system. I’m sending a team on it now, engineering out.”

“This is the bridge, comms check on omni bravo,” a young ensign pony standing at tactical said.

“This is Spacecomm watch. We read you lima charlie.”

“Roger, Spacecomm. Patch us through to 287’s NOC. Equestria out.”
“Captain on the bridge!” A pony sitting at Ops announced, as she abruptly rose to her feet, snapping to attention. The bridge went silent as everyone quickly went to attention.

Applejack scanned the bridge as emotionless faces stared back at her, yet she could feel the uneasy anxiety most ponies felt before a mission: the longing to get underway, and the apprehension of what lies beyond.

“Carry on, y’all,” Applejack replied, and everypony resumed their tasks. Applejack’s eyes fixed on the young mare at Ops. “Ensign Harvest, what’s the status on our departure?”

“Right on schedule, captain,” she replied with confidence. “I’m just rerouting some cargo to Cargo Bay Two. A Lieutenant JG Lyra brought on some rather bulky and sensitive equipment.”

“Yes, the astro-paleontologist and astronomy departments will be conducting experiments in sector 025.”

“No problem, Captain. It just needs some extra precautions.” She nodded nervously, her golden-orange fur turning red around her cheeks.

“Ensign Harvest, Divisional Officer of Logistics and Operations, your instructors spoke very highly of you,” said Applejack.

Berry Harvest nodded earnestly. “Yes, Captain. I graduated from the academy with distinction, and I couldn’t be happier to be on the HMS Equestria.”

“Well, ensign, welcome aboard. I can see you are already doing a great job. Will you coordinate with the logistics LCPO about Lyra’s cargo, and then join us in the observation lounge?”

“Yes, sir—ma’am—Captain.” Ensign Harvest clapped a hoof over her mouth as her face matched her red uniform.

Applejack raised an eyebrow. “Just ‘Captain’ will do.” Applejack cracked a sympathetic smile. “Don’t sweat it, Ensign. It happens to the best of us.”

Ensign Harvest nodded, and the red hue dissipated from her cheeks. “I’ll have something prepared for the meeting.”

Applejack held up a hoof, shaking her head. “That won’t be necessary, Ensign. This isn’t a formal briefing. Just bring everyone up to date on your department.”

“Aye, Captain.” Ensign Harvest sat at her console and began tapping various buttons. “Work transfer sent. I will join you when chief acknowledges the cargo transfer from Lieutenant Lyra.”

Applejack nodded. She walked across the bridge, stopping to stare at her chair. Its new, firm, tan leather cushions inviting her to sit; it was all hers.

After a good long look, she crossed to the other side of the bridge and entered the conference room.

Sitting at the long, slightly-curved table were her senior officers, her main crew, her friends. They were talking so loudly they didn’t hear her walk in. She took the moment to admire her crew in their newly-pressed uniforms: Twilight in her command red and three shiny pips on her collar, and her purple mane was up in a tight bun; Pinkie Pie in her yellow uniform with her mane crazy as always; Rarity, also in yellow with her mane in a stylish bun, and thick horn-rimmed glasses on her face; Rainbow Dash in red and Fluttershy in blue looked the same as ever to Applejack.

“Oh yeah! Well, you weren’t there when I out-maneuvered two Romulan Warbirds!”

“Oh don’t be silly, they were shuttles and you know it! There’s no way your ship could—”

“They were scout ships, Rarity. According to the after-action report, she employed some very complex and ingenious maneuvers to confuse them and escape,” Applejack said, bringing the debate to an end.

“Attention on deck!” Rarity said rising to her feet.

Pinkie Pie, Twilight, and Fluttershy all stood up. Rainbow Dash hastily stood up a second later after Fluttershy nudged her.

“Alright, y’all, sit down. We ain’t doing that formal stuff now. This is just a quick mission briefing anyway.” Applejack took a seat at the head of the table.

“But we already know the mission,” Rainbow blurted out.

“There’s more to it. As soon as our new operations’ officer joins us, we will get started.”

“I heard she’s really junior,” said Rainbow.

“She is, but she was the best in her class, and she came highly recommended from the detailer. She’s head of the department, handling all ship’s operations with”—Applejack looked at Twilight— “with your guidance, of course. I have a hunch you’ll like her.”

“What’s her name?” Rarity asked.

“Ensign Berry Harvest.”

“Doesn’t matter, her name is George,” Rainbow said, as she clapped her hooves together and an evil grin crept across her face. “Oh, I’m going to have her running all over the ship.”

Applejack sighed. “This isn’t the Wonderbolts or the Equestrian Planetary Defence. Starfleet takes hazing seriously. So please make her feel welcome.”

Rainbow Dash smiled nervously. “I was just kidding. I-I would never...I-I’m sorry.”

Applejack could almost feel how ashamed Rainbow Dash felt as the atmosphere in the room changed. “Of course you wouldn’t... First day on the job and such—its got me all wound up.”

“I know just the thing!” Pinkie Pie bounced out of her chair to the food replicator. “Chocolate cake, three layers with extra mousse filling and apple cider!”

“Specify type of cider,” the computer replied.

“Sweet Apple Acers style, non-alcoholic, seven bottles.”

The computer beeped in acknowledgement. A few seconds later, a tall cake and bottles of cider materialized.

“Everything's better with cake!” Pinkie Pie bounced around the room, passing everyone a bottle of cider.

“Well I’ll be damned…” Applejack said after taking a sip. “It tastes almost as good as the stuff back home.” She bowed her head momentarily.

“Of course! I programmed it into the replicator as soon as I came aboard.”

“Oh, you did that on the Hood too,” Fluttershy piped up. “The captain was very pleased.”

“You two were on the Hood together?” Rainbow asked. “Isn’t that the flag ship?”

“One of them, yeah, but the admiral wasn’t on it very much,” Fluttershy answered. “I was the junior surgeon aboard, and Pinkie was the junior engineer. But she probably should have been the chief engineer, since all of her inventions confused the engineering staff but always seemed to work anyways.”

“You guys got all of the cool assignments. Equestrian Planetary Defence my flank! If you want the most boring position in the universe, go there! Thank Celestia, Starfleet let me transfer...”

Rainbow Dash trailed off as the door opened and an orange mare with a bushy sandy-blonde mane walked in. She quickly scanned the room, her eyes lingering on the now half eaten cake on the table, then turned to Applejack.

“I’m sorry for the delay, Captain. I had to sort out a supply issue with sickbay.”

“S-sickbay?” Fluttershy squeaked.

“We almost received a shipment of standard biobeds instead of the shorter pony biobeds. All has been taken care of, doctor.”

“Everyone, this is Ensign Berry Harvest.” Everyone waved and nodded. “As you can see, she’s on top of it already. Ensign, let me introduce you to everyone. Over there is Lieutenant-Commander Pinkie Pie, Chief Engineer—”

“Hi, so happy to meet you! Have some cake and cider!”

“And,” Applejack said sternly, talking over Pinkie Pie’s hyperactive voice. “Next is Lieutenant Rainbow Dash, our conn officer. The one over there with the purple mane is Lieutenant-Commander Rarity, Chief of Security; and Commander Fluttershy, our Chief Medical officer, and last but not least, Commander Twilight Sparkle, our First Officer.”

“Welcome aboard,” Twilight said with a smile. “If there’s anything you need, don’t hesitate to ask. I trust indoc went well?”

Ensign Harvest nodded. “It did.”

“Glad to hear. I designed the course myself.” Twilight smiled, sounding pleased with herself.

“Alright, now that Ensign Harvest is here, let’s talk business. First, I want to say that with the exception of Ensign Harvest, we are all friends long before we joined Starfleet. Now this can make it a bit strange, as far as protocol is concerned. I’m in favor of loosening it later, but for now let’s keep it by the book—at least until we leave spacedock. After work we are friends, at work we… well, we have a job to do. Use your best judgement.

“Now, that that’s out of the way, and before I go into details about our mission, Ensign Harvest, will you please brief us on the cargo situation.”

Ensign Harvest stood up nervously. “I’ve been coordinating all approved cargo coming onto the Equestria. Most of it has been materials to refit the ship for ponies, as we aren’t as tall as most bipeds in Starfleet. Sickbay was the last to be refit, and it should be done soon. They’re working really fast.

“Aside from that, we picked up some sensitive scanning equipment to catalogue and collect some volatile nebula gasses and background radiation. There’s also a particle accelerator for testing the samples collected.” Ensign Harvest finished her report with a gasp for air as she hastily sat down again.

“Thank you, Ensign,” Applejack said with a cordial tone. “Now these things aren’t dangerous, but they are sensitive, and the materials they collect could be hazardous. Hazmat has assured me they have taken every precaution.

“As y’all know, we are surveying a remote sector near the Beta Quadrant; there are a couple nebulae, and Starfleet believes life could exist in the sector. Officially that’s all we are doing, but we’ve been given a few extra missions.” Applejack nodded to Twilight.

Twilight cleared her throat. “The Federation recognizes Princesses Celestia and Luna as heads of state, but they are still having trouble accepting any directives they have for the Federation—as they do with most foreign governments who remain with autonomous membership; however, Starfleet has allowed the Equestria to accept Celestia’s directive: Spread the magic of friendship,” Twilight said.

“I will have that added to our general orders,” Applejack said. “The last thing we have to discuss is another mission from Starfleet. This portion of the meeting is classified. There will be no mention or log of it anywhere until directed to do so.”

“Computer, seal the room, security level top secret,” Rarity stated.

The computed beeped and responded, “Warning, communications with ship’s functions will not be possible while this room is sealed.”

“Acknowledged. Seal the room,” Rarity restated, and the computed beeped, accepting her command.

“This briefing is classified top secret SCI,” Applejack said in a hushed voice. “The mission comes directly from the Office of Starfleet Security, so we can only accept orders from them as the controlling authority. And as of now, they say no discussing or logging of this mission, except in secure locations, and only with those who have need to know and are briefed.”

Applejack paused with a bated breath as all eyes locked on her. “The real mission is covert surveillance. Home Front is gaining momentum, and Starfleet believes them to be behind the devastating attack on the Lambda Two science outpost that killed three Starfleet officers.”

“Home Front!” Rarity huffed. “What do they want now?”

“Starfleet reform, less aliens, less exploration and more weapon development—the usual paranoid rhetoric,” Rainbow Dash explained feigning boredom.

“Lots of genetic material went missing from the lab too,” Fluttershy mentioned. “It could be used to create biogenic weapons.”

“As infamous as Home Front is for their propaganda and countless attempts to divide the Federation, Starfleet Intelligence has reason to believe a small group had became radicalized. No one can confirm they are responsible for the attack, or what they’re end-game is… but we could be looking at a coup—worst case scenario,” Applejack replied. “We are to survey them as covertly as possible, find others who sympathize with them, that’s it.

“I must remind you, this cannot be disclosed to rest of the crew until directed to do so. One of the science labs has been sealed off. That is where we will process all data for this mission. All further meetings regarding this mission will be held in there,” Twilight said.

With a last swig of her cider, Applejack stood up, giving Rarity a nod.

“Computer, remove secure shielding,” Rarity commanded.

The computed beeped. “Secure shield removed. All communications have been restored.”

“Let’s get this ship underway,” Applejack said as everypony filed out of the conference room.

Applejack stepped out onto the bridge. Twilight took her seat next to the captain’s chair where she began typing on her console.

“All departments checking in, Captain. Everyone is present and accounted for. All working parties have completed their assignments and non-crewmembers have disembarked,” Twilight said.

“Departure stations y’all,” Applejack ordered. “Ensign, open a channel with the dock master.”

“Channel is open,” said Ensign Harvest.

“Control, this is Captain Applejack of the HMS Equestria, requesting permission for departure.”

“Equestria, this is Control, you are cleared for departure,” a brisk female voice responded seconds later.

“Ensign, clear all moorings. Helm, thrusters to stationkeeping,” Twilight instructed.

“Thrusters at station keeping. Helm reads moorings cleared,” Rainbow responded.

“Maneuvering thrusters ahead. Take us out, Lieutenant.”

“Departing holding gantries. Speed, eighty KPH. One kilometer until space doors,” Rainbow reported.

“On screen,” Twilight ordered.

Applejack watched the flashing guide buoys disappeared under the view screen. she smiled as the ship approached the twinkling stars mere meters beyond the doors. To go from a finite space to the literal infinite had always left her feeling small, like a needle in infinite wonder.

The ship cleared the confines of spacedock, and everyone was greeted with the soft blue hue of Earth against the stark black of space.

“We have cleared spacedock,” Rainbow reported.

“Ahead full,” Applejack said softly. “Adjust course to exit vector bearing zero-zero-one mark two-five.”

Moments later, the blue planet below glided out of the view screen as the ship changed course, speeding out of the solar system.

“You’ve got to hand it to the Humans,” Rarity said thoughtfully, “They have a pretty planet.”

“Indeed,” Twilight agreed. “Similar atmosphere to our own, which is why Equus has the same blue color to it.”

“Engineering reports warp speed available,” Pinkie Pie’s voice said over the comm.

“Rainbow, lay in a course bearing zero-zero-two mark three-five, warp seven,” Twilight ordered.

“Course and speed laid in,” Rainbow replied.

“Engage,” Applejack commanded.

The stars on the view screen blurred in a mass of white as the ship broke the warp barrier, and they streamed by in blurred strings of light.

Applejack punched the internal comm button on her console. “Attention in the ship, attention in the ship. We are underway.”

“I can’t feel any vibrations in the deckplates,” Rarity muttered. “Such a divine ship.”

“Eh, give me an Equestrian fighter. You can really feel the engines on those bad boys.”

“Those hardly qualify as a ship,” Rarity retorted.

“I’m sending for all department heads to adjust duty rosters and watches accordingly,” Twilight added to Applejack, ignoring the debate between her friends.

Applejack nodded. “Rainbow,” she said loudly, cutting across Rainbow Dash’s counter argument. “Time to starbase 287?”

“Two weeks, present speed,” she replied.

“Maintain speed.” Applejack stood up from her chair. “I’ll be in my ready room. You have the bridge, Twi.”

Captain’s personal log, stardate 42286.54.

The ship has gotten underway without hitch. I’ve been feeling the stress and burden of command already. It makes me wonder how I’ll hold up under real stress.

It’s a good feeling to be serving with familiar faces. Starfleet was leery of us running a ship, no thanks to Home Front, but I believe us ponies can hold our own like any other Starfleet crew. We’ve all served well on other ships and—

The door chirped, interrupting Applejack’s log entry and wall-to-wall pacing. She quickly returned to the chair behind her desk. “Come in.”

The doors opened to the outline of a purple unicorn wearing a ‘we need to talk’ expression. It was an expression she had seen before, and she had a pretty good idea what Twilight wanted to talk about.

“Twilight…” Applejack trailed off, unsure how to proceed; so, she opted to say nothing and let her talk.

“Applejack, are you feeling alright?” Twilight asked gently, taking a seat across from Applejack.

“Yeah, I’m—” Applejack stopped herself under Twilight’s unconvinced stare. “Sometimes getting out of spacedock, especially at headquarters, can be more stressful than coming nose to nose with a Romulan warbird.”

Twilight said nothing, fixing her gaze on the stars streaming by behind Applejack. “I suppose… this is my first time on a ship since I was an ensign. I-I just came by to see if you’re doing alright,” Twilight said softly.

“I’m fine, Twi. I can handle it.” Applejack slumped back in her chair. Sensing Twilight’s hesitation, she spoke. “The question is, Twi, are you feeling alright?”

Twilight gulped and shifted in her chair. “I wanted to thank you for asking me to be your first officer…”

“... but you think I should have picked someone else,” Applejack said, completing the unicorn’s sentence.

Twilight nodded.

“You are the rank of commander, and you’ve been a first officer before,” Applejack said with a frown. “I think you’re plenty qualified. I was actually a bit shocked you weren’t promoted to captain too.”

“I was the first officer of the Starfleet Institute of Science by default. It was a captain and myself among twenty civilians, and all we could do was advise them; we had no real authority. I was there most of my career. I served on one science vessel as an ensign,” Twilight finished, looking down at the desk in defeat. “I request Rarity be appointed the first officer.”

“Request denied.” Applejack smiled warmly. “I’m glad to have you as my first officer.”

Twilight cocked her head to one side. “But I’m not experienced in starship—”

Applejack held up a hoof silencing Twilight instantly. “Exactly. You’ll bring something new to the same old routine. And,” she said forcefully to silence Twilight objections, “you already have, like making that indoc course. No one’s done that. Everyone uses the same standard Starfleet one that has everyone sound asleep in minutes. We used to take bets on how long it’d take for someone to doze off. You delegated watchstanding authority to the department heads… another thing not done on a ship, but I agreed because it makes more sense. Twi, you’re already doing amazing work and we’ve just started.”

For a brief second all that could be heard was the hum of the ship and the occasional beeps from Applejack’s computer.

Twilight, looked up, doing her best to keep an even expression. “I-I didn’t realize… all of those things I did, just made sense to me.”

“Just keep it up. After a few days, all that ship stuff will come back to you, I promise.”

Twilight nodded earnestly. “I was just a little… flustered, coming back to a normal Starfleet working environment.”

“Ain’t nothing to worry about. There is no precedent for an all-pony crew. Which means, we get to make it.” Applejack flashed a reassuring smile at Twilight. “Don’t sweat it, Twi. I’ve read your papers, talked to your former COs, and I’ve known you for the longest; I know you have it in you.”

“You’re right. Maybe it’s this…” Twilight gave Applejack a nod and lowered her voice, “this mission that has me on edge.” Her eyes shifted nervously. “Charting new territory… that’s pretty big!” Twilight added hastily.

Applejack silently agreed, but said nothing. Instead she offered a sympathetic smile. “Well, I guess it’s about dinner time. Would you like to have dinner with me in Ten Forward?” Applejack asked.

“Sure,” Twilight responded happily.

When the word had gotten out that Pinkie Pie programmed Sweet Apple Acres cider into the replicators, replicator use became so taxing on the power system, the cider had to be restricted to only Ten Forward. It only took a few minutes for the news to circulate the ship, and ponies flocked to Ten Forward. By 1700 hours, there wasn’t a pony on the ship who didn’t know, and to Applejack’s great annoyance, Ten Forward was more packed than the Grand Galloping Gala.

“What in tarnation…” Applejack mused aloud. “Dang that Pinkie Pie.”

“She just can’t keep a secret, can she?” Twilight fought her way through the sea of ponies standing around talking in loud and excited voices; unicorns took to levitating their drinks high above their heads to avoid spilling them. After several minutes of careful maneuvering, they made it to the bar.

As far a Applejack could see, there wasn’t a single open table. “I guess it’s good everyone is socializing and all, but you might want to advise the department heads to alternate meal times,” Applejack suggested, shooting Twilight a stern look.

“You could sound general quarters, captain, that ought to get them out of here real fast,” the mare behind the bar said slyly. She was pale-purple with a berry-stained red mane. Her mane was frazzled and her eyes sagged.

“The name’s Berry Punch, Captain,” the mare added. “I run Ten Forward.”

“I believe I know you from somewhere,” Twilight said, her eyes lighting up with realization when the mare said her name. “If I could just…” She screwed up her face in concentration.

“Well, I’m from Ponyville, Commander. Maybe there.”

“Ponyville!” Twilight exclaimed. “Yes, I lived there before joining. That’s where I know your name from.”

“Well, Miss Berry Punch, your idea is tempting, but I can’t do that,” Applejack said.

“But you have to admit, it’d be funny to watch them scram at the sound of an alarm.”

Applejack chuckled, but of course she wasn’t going to torment her crew with false alarms. Most times it led to court martial—as one trickster ensign found out on her last ship. “But then you’d have to clean up all of that broken glass.”

Berry Punch nodded thoughtfully. “Touché, Captain. Anyway, what can I get you two?”

“Um, I’m not all that hungry. I’ll just have a dandelion salad,” said Twilight. “And tea, green tea.”

“Green tea?” Berry asked, cocking her head.

“It’s a Human thing. It’s really soothing and high in antioxidants.”

“Interesting,” Berry said in a flat tone. “And for you, Captain?”

“I’m starvin.’ I’ll have a double hay burger and a bottle of my cider.”

“Coming right up.”

Applejack turned to Twilight, who appeared to be scanning the room for an open bit of floor to stand. “I guess we can just eat here at the bar,” Applejack suggested.

“Yea—”

Twilight was cut off by a rainbow colored blur zipping across the room, high above everyone’s head, stopping inches from Twilight.

“Sorry, Twi—Commander,” Rainbow Dash said, backing up slightly, but still continued to hover at head-level. “It’s really crowded in here.”

“I hadn’t noticed,” Applejack deadpanned.

Berry Punch returned with Applejack’s and Twilight’s orders.

“Hey, Berry, can I just get a cider?” Rainbow Dash asked, not bothering to keep a tone of urgency out of her voice.

“Where are you goin’ in such a rush?” asked Applejack.

“Holodeck for a Wonderbolts flying program.”

“Interesting,” Twilight said. “I’ve only used holo projectors to make three dimensional models. I’d be curious to see a fully rendered computer environment.”

“You can join me after you eat, if you like. You too, Captain.”

“Certainly!” Twilight said cheerfully, and she began to eat with gusto.

“I’m alright. I should probably check in on Apple Bloom and see how she’s doin’.’”

After finishing her meal and feeling the onset of ‘too many carbs’ fatigue, she wished Twilight and Rainbow a fun adventure on the holodeck and left Ten Forward.

The turbolift doors opened to her deck, greeting her ears with the sound of muffled music. She couldn’t tell where the music was coming from, but it was way out of regulation.

Applejack continued down the corridor, determined to find the source of the music. Normally, she’d rather not intervene, but since it was the officer’s deck, and she was wanting to relax—Applejack stopped dead. The music was loudest from the door she just passed, her own.

The doors opened to her proximity, blasting her ears with clattering and howling noises. The instruments were of percussion mostly, but they were of different tones that clashed horribly.

“Computer! Turn off that damn noise!” Applejack shouted at the top of her lungs. The music ceased, leaving a ringing sound in her ears. The spare bedroom door opened and the culprit came striding out. “Apple Bloom! What in tarnation were you listening to?”

“Klingon.” Apple Boom shrugged.

“That ain’t no Klingon music… a headache more likely.” Applejack rubbed her temple. “ And why were you blasting it to all of deck eight?”

“Apparently at the right volume you can hear the rhythm of a Targ’s heart.” Apple Bloom rubbed her head. “But I think it’s just noise at all levels.”

Applejack shook her head. She pushed past her sister and plopped down on her couch, stretching out. “Apple Bloom… please keep music at a reasonable level. If you want to find hidden Klingon messages in music, take it to the holodeck,” said Applejack as she unzipped her uniform and disrobed. “And who said you could hear a Targ’s heart beat in that… song?”

“Kaz-Mara,” Apple Bloom muttered.

Applejack raised an eyebrow.

“What?” Apple Bloom asked. “It made sense to me! The band is called The Heart of the Targ.”

“Ain’t that the same Klingon boy who tried to scare you by eating live gagh in front of your face?”

“Then he threatened to eat me because it didn’t gross me out,” Apple Bloom shot back.

Applejack snorted. “Typical Klingon.”

“He tells all kinds of crazy war stories; they’re all really interesting too. I guess he got me with this music prank…” Apple Bloom trailed off. “So anyway, how was your first day, sister Captain?” Apple Bloom asked, taking a seat.

Applejack flashed her a smile and a wink. “It ain’t nothin’ I can’t handle.”

Captain’s log, stardate 42320.94

After two weeks, the crew has fallen into routine. They have performed as well as any captain could ask; only time will tell how they will really hold up as danger looms on the edge. We are due to arrive at starbase 287 in one hour, and I for one, will be happy for a change of pace and scenery.

“Captain,” Ensign Harvest began. She half turned, giving her console a skeptical look. “I’m getting strange subspace readings. Possibly a subspace transmission.”

Applejack frowned. “Can you be more specific, Ensign?” she asked, checking her console.

“There’s a massive subspace distortion dead ahead with a very distinct oscillation.”

“Confirmed,” Rarity said. “It appears to be a subspace transmission, but the source and destination aren’t apparent. It’s definitely not a Starfleet signal.”

“Is it a ship?” Twilight asked.

“Unknown,” Rarity answered.

“All stop,” Applejack ordered.

“Aye, Captain,” Rainbow Dash answered. “Reversing engines… we are now holding position.”

“Captain, recommend we go to yellow alert,” Twilight added.

“Do it.” Applejack nodded. “Rarity, can you get a fix on the location?”

“I have the coordinates where it was detected, but it is no longer there.”

Spatial coordinates flashed on Applejack’s console. “Rainbow, ahead slow bearing five-zero-zero mark zero-zero-five.”

“Aye, ahead two hundred KPH.”

“Ensign, signal starbase 287, and tell them we are investigating a localized anomaly and will be momentarily detained.” Applejack sat back in her chair, fully appreciating it for the first time. In the uneventful two weeks, it had never felt quite right.

“Arriving at the coordinates,” Rainbow Dash informed.

“All stop. On screen,” ordered Twilight.

The view screen flicked on, revealing nothing but empty space.

“Anything?” Applejack asked.

“Nothing,” Ensign Harvest responded. “And I mean nothing. If a ship were here, there’d be ionized particles or some kind of warp signature.”

“Captain.” Twilight turned to Applejack, giving her a serious look. “Recommend we continue scanning the area, carefully. To distort subspace like that requires a lot of energy. I think it’s still here… somewhere.”

“Agreed, but we can’t delay too long. Commander, work with Ensign Harvest, I want a briefing in fifteen minutes.”

“Aye, Captain,” Twilight replied. “Ensign, we need to adjust the lateral sensor array to scan subspace for localized distortions.”

“What are we looking for, Commander?” Harvest asked, as she rose to her feet.

“I’m not sure yet, but I have a suspicion. We can use the primary sensor terminal in main engineering.”

Twilight and Harvest left the bridge.

“Rainbow, prepare to take us back on course shortly. Rarity, you have the bridge.”

“Aye,” they replied in unison.

“Now, Lieutenant Dash—”

The conversation cut out as Applejack’s ready room door shut behind her. She sat behind her desk, opening her computer. Hoping to review long-range sensor data sent over from Starbase 287.

“Captain, this is Engineering!” A hyper-active voice squeaked over the intercom.

“Applejack here,” she responded.

“Oh goodie! Twilight and Berry here want to take the impulse engines offline so they can channel the power into the short-range sensors.”

“Twilight and who?” Applejack scratched her head.

“Oopsies. Commander Twilight and Ensign Harvest want—”

“Twilight here, Captain. We need to boost the frequency beyond what the ship is normally capable of giving the sensors.”

“Pinkie?” asked Applejack.

“Not to worry captain, it will work, we just won’t have impulse power. Warp drive will still operate!”

“Alright, proceed, Commander.”

“Okie dokie loki, Captain. Chief Engineer Pinkie out!”

Applejack ran a hoof through her mane. “I need cider.” Crossing the room, she paused to look out the window at the stars, gleaming in the distance.

“Computer, warm cider,” Applejack muttered. “With a dash of cinnamon in it.”

The console hummed and a mug materialized. The aroma of apples and cinnamon filled the air, making Applejack hum in content. “Ain’t nothin like a warm mug of cider and gazing at the stars.”

Reluctantly, she returned to her desk. “Computer, transfer all of Starbase 287’s long-range sensor logs to my computer and identify any anomalous readings.”

“There are three-hundred and sixty anomalous readings.”

“Identify any that could be caused by a ship’s engine or a ship’s weapons.”

“No anomalies fit specified parameters.”

“Hmm… Computer, are there any readings similar to the subspace distortion that was detected by the ship?”

“Affirmative.”

“Well that’s something,” Applejack said to herself. “Computer, display data.”

As data began to appear on her screen, Applejack overlaid a spatial grid, so she could correlate the readings with a location. The entire grid was speckled with dots and corresponding dates. Applejack enhanced a section, and the dot turned into to a sine wave of an extremely high frequency and amplitude.

“That almost looks like a communication carrier wave.”

The intercom beeped and Twilight’s voice sounded through the computer. “Twilight to Captain, we found something. You might want to come down and take a look at this.”

“I’ll be right there.”

On the bridge, Rarity and Rainbow Dash seemed to be in the middle of another debate; they were unaware of the other crew member’s annoyed glances or that the Captain had stepped onto the bridge.

“No, Rainbow, even us ponies have to adhere to some standards. Being the only quadrupeds in Starfleet, and one of the only races who don’t wear clothes, makes it difficult, but the uniforms for us aren’t that bad. In fact, I think they’re quite nice.”

“You’re only saying that because you designed them,” Rainbow Dash shot back.

“Well, someone with design sense had to—”

“Captain on the bridge!” A young ensign stallion shouted over Rarity.

Applejack shot Rarity and Rainbow Dash a strong look as they shifted in their seats. “Commander, put us back on course,” Applejack said as if nothing had happened.

“Yes, ma’am,” she replied. “Lieutenant, bring us about bearing five-zero-zero mark three-zero, ahead warp seven and engage.”

“I’ll be in engineering.” Applejack stepped into the turbolift; however, before the door shut, she placed her hoof in between the turbolift and the bridge. “Oh and, Commander?”

“Yes?” Rarity replied.

“If y’all want to debate Starfleet policies, I’d appreciate it if you kept it off my bridge.”

“Yes, of course, Captain. It won’t happen again.”

The doors closed, and the turbolift hummed to life after Applejack announced her desired location.

The engine room hummed rhythmically to the pulsing of the warp core. A blue hue flashed in time with the oscillating sound.

Pinkie Pie bounced out of an access hatch. “Lieutenant, bring the impulse engines back online!” Pinkie sang. Her eyes widened when they landed on Applejack. “Ooh, Captain! Goodie you’re here. Twilight found something.”

“Indeed,” Applejack responded. She visually scanned the main room, spotting Twilight and Harvest hunched over a console.

“But, Commander, that’s impossible,” Harvest said in a hushed voice.

“But the data says it right here,” Twilight countered.

“It must be wrong,” Harvest insisted.

“Report,” Applejack stated, causing both of them to startle.

“What our sensors detected was a glimpse of a message relay station. It’s normally hidden in subspace and uses a multi-phased field emitters to stay hidden from conventional sensors.”

“Then how did we detect it?” Applejack asked.

Ensign Harvest smiled, as if she was waiting for someone to ask the obvious question. “I think it’s because its power output spiked to relay a really big datafile.”

“The messages use a very strong encryption, the computer can’t make any sense of it,” Twilight continued on. “Cryptography isn’t my area, but I think the ship’s computer isn’t powerful enough to try decoding it.”

Applejack frowned. “What could be used to generate this type of encryption?”

Twilight shook her head. “Computers with an unimaginable computation speed.”

“Can we disable it, or destroy it somehow?”

“That wouldn’t be too hard, but if my calculations are correct, there are at least ten more of these things in a two light year radius, maybe more. These things are virtually undetectable, unless they are processing some sort of data it seems. During my scan, I noticed small subspace distortions, but they’d vanish almost instantly.”

“Are you suggesting this is some kind of secret communication network?”

“We are,” Ensign Harvest said. “We cannot identify the source or destination, but we do know that heavily encrypted messages are being sent somewhere.”

Applejack sighed. “Good work, you two.”

“Bridge to Captain,” Rarity’s voice sounded over hum of the engines.

“Applehack here.”

“Captain, we’re approaching Starbase 287.”

“On my way,” Applejack replied. “Ensign, start compiling this information into a report for Captain Hawkins and his staff.”

“Aye, Captain.”

“We’ll be on the bridge.” Applejack and Twilight left the main engineering section.

“Report,” said Applejack as Rarity stood up and offered her chair back to Applejack.

“We just dropped out of warp. We are approaching Starbase 287 at one-quarter impulse power,” Rarity informed.

“On screen,” Twilight ordered, and moments later a massive sphere with a thick ring around its equator where many arms reached out to saucer-like sections appeared. It nearly filled the entire screen; only a few stars could fit in the frame.

“Not bad,” Rainbow commented. “I thought this was going to be smaller.”

“One of the only outposts out here…” Applejack said, mostly to herself.

“Captain Hawkins is hailing,” said Rarity.

The screen clicked on, and a dark-haired man with bright blue eyes came into focus. He was sitting behind a massive wooden desk in, what Applejack could only guess was his office, but the space seemed to be bigger than her bridge.

“Captain Applejack of the HMS Equestria, I see you made it alright.”

“Everything went off without a hitch,” Applejack replied.

“Almost… Captain, will you and your first officer beam directly to the station? That little investigation of yours put our schedule in a bit of a crunch.”

“We’ll be right over, Captain.”

The channel closed abruptly after, leaving the bridge in dead silence. Everypony was looking at Applejack except Twilight who was still staring at the view screen with a perplexed expression.

“Captain…” Twilight began.

“Not now,” Applejack held up a hoof. “Rarity prepare the ship for docking, you have the bridge until we return.”

“Aye, Captain.”

“And tell Harvest to coordinate the provisions needed for our mission.” Applejack leaned in close to Rarity, lowering her voice. “Tell her there’s a special list in the lab.” She quickly stood up and walked to the turbolift doors, Twilight close behind her.

“Transporter room one,” Twilight chirped to the elevator console. “So… Captain Hawkins… care to elaborate?”

Applejack couldn’t help but pin her ears. “Not really,” she spat, but Twilight’s raised eyebrow drilled into her. “Look, it ain’t nothin’ to worry about. We butted heads a few times at the academy… been enemies ever since.”

“I see,” Twilight said softly.

“He’s a good captain. It pains me to admit it, but I’d be a fool not to.”

They entered the small circular transporter room and stepped onto the pad. ‘Energize,” Twilight said to the transporter chief, after they stepped onto the pad.

The tiny room dissolved in a flash of blue light, and another small room came into focus. It was similar to the ship’s transporter room in many ways, except this room was full of humans.

Applejack didn’t recognise the younger officers, but she recognized the taller, older one in the middle. He stood with his hand on his hips, and he kept his head angled upward. Applejack could only guess he did this to assert a dominant posture. Not that it was needed since she only came up to his midriff.

“Captain Applejack,” Captain Hawkins said.

“Captain Hawkins, it’s been a long time…” Applejack stepped off the transporter pad. “May I introduce my first officer, Commander Twilight Sparkle.”

“Welcome to Starbase 287,” he said lightly, nodding to Twilight. “This is my first officer, Commander Scott and the station’s intelligence officer, Lieutenant Nichols.”

“I’ve read some of your papers, commander,” Commander Scott said. His voice was eventone and soothing, compared to the almost aggressive tone of Captain Hawkins. “Very insightful. If there’s time after, I’d like to share some ideas on quantum mechanics.”

“Um, c-certainly, Commander,” Twilight stammered, taken aback.

“Now that that’s out of the way...” Captain Hawkins clapped his hand together, focusing his eyes on Applejack. “Shall we go to the conference room without anymore… delays, Captain.”

“We’ve made an interesting discovery less than a light year from here,” said Applejack. “My Ensign is sending the details in her report.”

“That’s… interesting,” Captain Hawkins said slowly, almost sneering.

Despite his tone, Applejack decided not to bite and stick to business. If he wanted to drag up the past, he could lament about it after hours.

“This is pretty exciting,” Commander Scott said. He was either ignoring the Captain’s attitude toward Applejack, or completely oblivious. “This is my first time meeting anyone from Equus.”

“There aren’t too many of us in Starfleet, and most of us are now on one ship,” said Applejack.

“I’ve heard about both of you, of course. Captain Applejack, the first equine captain in Starfleet, and Commander Twilight, whose research in quantum mechanics has been ground breaking.”

Commander Scott stared between Applejack and Twilight with intent. “I used to be a science officer, back in the day when Starfleet vessels had those. I switched to command a few years back…”

Soon Commander Scott’s small talk blended with the white noise of the station as he droned on from one topic to another. He didn’t seem to care or notice no one was really listening. Applejack was left wondering how far the conference room was.

“Say, isn’t it true your people, ponies, don’t normally wear clothes?” asked Commander Scott.

“It is,” Twilight chirped. “We only wear clothes on occasion. Adjusting to wearing a uniform everyday was something strange for most of us. Only the ponies who transferred from the Equestrian Planetary Defence or the Wonderbolts didn’t have trouble adjusting.”

“Interesting. So interesting. Most bipedal species I’ve encountered have had some sort of modesty. It’s rare to encounter a nudist society…” Commander Scott trailed off, lost apparently in memories. “But none of those species were quadrupeds. …nor did they resemble the equines of earth. You are truly a unique race for this galaxy.”

Applejack was relieved to finally come to a halt in front of a door. The ten-minute walk from the transporter room to the conference room had felt like an eternity.

“Computer, open the conference room doors. Security clearance, alpha, pi, omega,” Captain Hawkins said.

“Voice print recognized,” the cool-female-computer voice replied.

The room was massive. The Equestria’s conference room resembled a closet in comparison. A massive black table spanned the long windowless room. A large view screen sat on the wall at the head of the table, and two smaller consoles sat on either side.

Applejack was so taken by the size of the room, she nearly missed the fact that someone was already seated at the end of the table. But it couldn’t be… there was no way—

“Spike!” Twilight shouted with glee.

“Twilight!” The purple dragon rushed forward, leaping into the air and wrapping his arms around Twilight’s neck, hugging her tightly.

“Oh, Spike, it’s so good to see you again,” Twilight said. A tear ran down her cheek.

“Well, I see you know our Starfleet liaison,” Captain Hawkins said as a satisfied smile crossed his face.

“Howdy there, Spike.” Applejack bowed her head.

“AJ, it’s been so long.” Spike released his death grip of Twilight to give Applejack a tight hug.

“Oh, I almost had you too!” Captain Hawkins said, laughing loudly.

“Wha—what?”

“Oh, you should have seen the look on your face!”

“Wait… you planned this?”

“Do you really think I’d still be upset over silly academy competition?” Captain Hawkins laughed. “Congratulations on making Captain! You finally made it.”

Applejack flattened her ears, as the pains of guilt rose through her chest. Yet even as she mentally kicked herself over her stubbornness, gratitude surged through her.

“Thank you,” she said bashfully. Being completely lost for words, she simply grinned.

“When we were requesting a ship and a liaison, I saw Spike had a transfer order in, and a newly commissioned ship and Captain were awaiting orders, so it all sort of worked out. Of course keeping the whole thing secret until you got here was tricky.”

“I had no idea which ship was coming here,” Spike added. “He just kept telling me, ‘it will be a ship you’ll like.’”

“Well, now that that’s out of the way… shall we begin the mission briefing?” Lieutenant Nichols said, speaking for the first time. His voice was wheezy and pitched.

“Yes, I suppose we should get this thing going.”

The console beeped, and seconds later an officer appeared on the screen. “Sorry to interrupt, sir, but a secure transmission is coming through from the Equestria for Captain Applejack.”

“I’ve been expecting that. Put it through, Ensign,” said Applejack.

“Captain Applejack, perhaps you’d like to start by briefing us on what you’ve found,” Lieutenant Nichols suggested.

As Applejack went into summarizing the report, she noticed no one seemed too surprised. They all seemed to nod as if some suspicion was being confirmed.

“I think they’ve found your Subspace Net, commander,” Captain Hawkins said.

“Subspace Net?” asked Twilight with her head cocked to the side.

“It’s only been rumored… hearsay and sensor echoes. This is the first piece of evidence that suggests it may actually exist,” said Commander Scott. “But supposedly there’s a massive repository of information on the Federation and Starfleet that interconnects several planets in some sort of hidden network, so Starfleet has no means of monitoring it.”

“This changes the nature of the mission,” Lieutenant Nichols said. “Instead of trying to crack the encryption, why not just follow the data?”

“To what end?” asked Captain Hawkins. “We’re not even sure this is anything related to Home Front.”

“We know data is being transmitted through this thing, and we know the encryption is beyond our cracking capabilities, so why not see where messages are originating from, or at the very least, find out where they are going?”

“I have to agree with you, lieutenant. Someone went to a great deal of trouble to move massive amounts of data quietly, and it’s in Federation space. If we can adjust our sensors to better detect these things, I suggest this be the Equestria’s first mission of poking around in this sector.” Applejack nodded to Twilight.

“Detecting these relays will be tricky, but not impossible. I already have some ideas on how to proceed,” Twilight informed as her cheeks grew a slight shade of magenta.

“Very good. I’ll relay to Starfleet Intelligence what’s been found and what you plan on doing, captain,” Captain Hawkins said. “I’m granting you the power to look into and investigate any and all Home Front activity, or suspected Home Front activity.”

Applejack nodded. “Understood.”

“Commander, if I may, I’d like to take a shot at cracking the data you captured,” Commander Scott asked. “I have a team of coders with nothing to do.”

“I’ll make everything available to you and your team,” Twilight replied.

Captain’s log, stardate 42325.88.

We’ve left Starbase 287, taking on an Equestrian attaché, by order of Starfleet and Princess Celestia. His job will be to successfully bridge the gap between our government and Starfleet.

Our next leg of the mission takes us along the relatively unexplored sector 280. Sensor scans haven’t been revealing, but we’re hoping for best. At least the astrophysics department is collecting on the unusual and seemingly random tachyon particles.

Applejack stepped out of the turbolift, making her way down the corridor. Science Lab Two had been sealed from the ship, and the door was removed, leaving a blank wall. As far as the ship was concerned, and the official ship map, Science Lab Two never existed; the space was simply listed as a ‘structurally reinforced bulkhead.’

“Computer, activate site-to-site transport, program AJ One,” Applejack muttered.

Without warning, or acknowledgement from the computer a bright-blue light swept the brightly light bulkheads of the corridor to a dimly-light room. Massive monitors on the wall gave the room a blue hue. Text sprawled across some of them, others displayed ship locations and spatial coordinates, and one displayed raw sensor data as it came in.

“Welcome to the Spatial Operations Center, Captain,” said Ensign Harvest.

“Good work, ensign.” Applejack strode over the circular console in the center of the room.

“I had the idea of running some high em scans from class three probes. In theory the scans should be bounced off or scattered by subspace distortions.” Ensign Harvest pointed to the monitor displaying raw sensor data. “I’m filtering out anything I think is suspicious…”

Applejack waited as Ensign Harvest let her sentence hang, but she didn’t elaborate. “And?”

“I haven’t found any more relay stations, but I did find something interesting.” Ensign Harvest tapped the console, and the raw sensor data display vanished. Instead a scatter plot of coordinates appeared. “I believed this to be a relay station until I realized it was moving.”

“A ship,” Applejack responded simply.

“A ship using a similar cloaking technology, normal sensors can’t see it… If you look here, Captain”— Ensign Harvest enlarged a dense part of the chart— “the ship was on a patrol of this area… but now?” She enhanced another section of the chart. “They’re headed right for us.”

“Have they detected our scans?” asked Applejack.

“Hard to say… they probably detected the high level em bursts from the probes… but even then, they’re not on a course to intercept the probe. They know we’re here despite our shield configurations.”

“What are you suggesting, Ensign?”

“I don’t think we are the only ones spying out here.”

Acknowledgments

Acknowledgments

Acknowledgments

Special thanks to everyone who has been a part of making this a reality.

Pre-readers

97xxfastbike

My awesome sister (no fimfiction account).

Preface

Preface

It hadn’t always been easy for the ponies… even after they were accepted into the United Federation of Planets, many years passed before they were accepted into Starfleet under the Ponies for Starfleet Initiative Program (PFSIP). It was believed the ponies would be too docile when push came to shove, but no one looked too closely into the history of Equestria. Or perhaps there was lots of misinformation about ponies at the highest levels. No one could find the source of the misinformation. Except for the members of PFSIP; they knew the truth... They were there in the beginning. They set the record straight, and ponies were allowed to serve in Starfleet.

Six heroes of Equestria were among the first to be offered entry into the academy. This is the story of where those six heroes are now…

Glossary

Glossary

George: A term used to refer to the most junior officer on board the ship. Often a George Ensign is assigned the most meaningless tasks as a form of hazing. Whereas the Bull Ensign is the most senior of the ensigns.

HMS: Her Majesty's Ship.

FITREP: Fitness report is an evaluation form for officers where their performance is ranked against other officers.

LCPO: Leading Chief Petty Officer. In most cases the LCPO is the most senior enlisted in a division.

Lima charlie: "I read you lima charlie," is a saying in radio communication meaning 'loud and clear.'

NOC: Network operations center. NOCs are places where networks are monitored and managed.

SCI: Sensitive Compartmentalized Information. SCI is a caveat used with classification of information, limiting access to those with the need to know and are read into specific programs.

Rank Abbreviations:

CAPT: Captain
CDR: Commander
LCDR: Lieutenant Commander
LT: Lieutenant
LTJG: Lieutenant (sometimes just called JG)
ENS: Ensign
CPO: Chief Petty Officer