Author's Note

This is the map of the ship, all areas adjacent have doorways between them unless noted with X:
-------------Storage 1==*==Medbay==Bathroom-X-Observation
-----------------||-------------------X----------------||----------||
Engines=Hallway==*===Kitchen====Bunks===Oxygen=*=Cockpit
-----------------||-------------------X---------------||------------||
-------------Storage 2=*==Electrical====Admin===Comms
Vents exist from Oxygen to Admin, Bathroom, and Cockpit; and from Electrical to Kitchen and Medbay. Only doors that go up-down or have a * are sealable.

Wakeup

Out in space near a reddish planet half the size of the familiar blue marble, a solitary metal ship resembling a turtle with three large engines in a triangular configuration coasted along. Inside the sleeping compartment, a light came on, illuminating a statue of Twilight, her friends, and Spike, in various poses stuck between the bunks.

Suddenly, Twilight's face cracked, and in moments, cracks spread across the statue, and out emerged Twilight, then Rainbow, Fluttershy, Pinkie, AJ, and Spike, all blinking groggily.

Rainbow coughed. "Ugh, rock dust. Well, at least we woke up. As nice as those dreams Luna gave us are, I feel like I haven't flown in months!"

Twilight giggled. "Technically, we've been flying through space the whole time. Granted, the engines have been off. Hopefully their nuclear reactor starts up again fine."

Rainbow winced as a white hoof poked out from behind her, then shoved her away. "Pteh, pteh, ugh, Rainbow Dash!" spat Rarity. "Did you have to put your derriere right in my muzzle as we got petrified?"

"Yep, I warned you before we got onboard not to hold us up on the launchpad, and well, how could Mr. Hiney not smooch a pretty mare who spent an extra 15 minutes on makeup! So how's it taste, like pure awesomeness?" Rainbow asked with a smirk as Pinkie giggled and high-hoofed her.

AJ promptly did the same.

"Blegh, absolutely not!" replied Rarity. "I need to wash out my mouth!"

Twilight stifled a giggle with her hoof. "Good to see the petrification hasn't affected our personalities. Now before you do that, Rarity, I need to remind us all of what we need to do."

Rarity groaned as Spike patted her hip, then hopped up on her back and gave her a massage.

Twilight cleared her throat. "So, this ship is bound to have issues after 9 months in space, and there's no rescue out here. We've all got tasks to complete to make sure everything important works. Checklists are available in the administrative office for each of you. We should have plenty of time before the insertion burn tonite, as the last automated report suggested only some minor malfunctuh...functions." Twilight grabbed her head as she swayed a little. "You're probably all feeling what I am, the aftereffects of long-term petrification. It messes mainly with the brain and nervous system, and can be highly variable. We'll all be back to normal within an hour or two, so don't rush. Make sure you understand what you need to do before you do it. You can go now, Rarity."

As soon as Twilight finished talking, Rarity rushed to a nearby doorway into an area with sinks, squat toilets, a bathtub, and showers, with Spike gripping tightly, barely staying atop her.

Applejack giggled slightly. "Ya know, I bet Rarity, bein' stubborn as a mule, didn't listen 'bout usin' the toilet before we left and is just sayin' she needed water as a cover! Anyways, ya think Equestria's doin' alright. Ya know, without us around?"

Twilight sighed. "I'm fairly sure that between the Pillars and the students, nothing too bad will happen. Anyways, there's no use worrying about it now, we just need to focus on dealing with the space changelings."

Pinkie popped up in front of Twilight. "And throw them a party!"

Rainbow facehoofed. "Yeah, I'm sure that'll work real well, Pinkie, way better than just kicking their rumps until we hear cracking noises."

Twilight rolled her eyes. "Remind me again why you were opposed to taking Garble and Lightning Dust? We're gonna be going up against some pretty powerful enemies if Luna's right."

Rainbow snorted roughly. "They're unreliable! All that talk about improving was just so they could impress Smolder and Ocellus. Besides, we've fought tons of tough stuff, we'll be fine."

AJ stretched like a cat, rump up as she straightened out. "Well then, let's get a move on instead of just chattin' all day. Some chores will do us well to get our heads cleared. And we'll need that like a tree needs sunlight if we wanna actually try and stop these space changelings."

Twilight nodded. "I don't know about that, but we'll need at least two sets of eyes on everything. Try to stick to what you know and focus on things we need right away, like oxygen and the electrical wiring. I'll be in comms to check messages and update you on problems I can see. We've probably got a message backlog, and hopefully it has some info on the threat we're facing."

Everypony trotted out of the room.

In admin, Fluttershy looked over the status lights on the ship's program units. "Finally..."

Twilight trotted into the doorway nearby from comms, and knocked a few times on the wall.

Fluttershy turned to face her. "Oh, what is it, Twilight?"

Twilight smiled. "Just wondering how you're feeling, 'cause I've got a headache."

Fluttershy frowned. "Oh I'm sorry. Well, I'm pretty tired of staring at computer memory and looking over folders of our files. Um...oh, I'm just having a bit of a tummyache." Fluttershy blushed and crossed her legs.

"I catch your drift. There's some potions in tiny little vials. I think the mild emetic is the one you want."

"Oh, but, it's not serious..."

Twilight rolled her eyes. "We've got plenty, Fluttershy, and I'd rather you do tasks a little later in ship shape than miss something."

Fluttershy nodded and trotted off through the bunk area, hearing a loud squealing that sounded like Rarity.

As she approached the bathroom area, there then came sounds of a fight.

Soon, Rarity ran out, spitting out water. "Ugh..."

Fluttershy raised an eyebrow. "Are you okay?"

"Let's just say...that that very strong bidet, has ruined my day, darling." Rarity turned and trotted away.

Fluttershy peeked in, and saw Pinkie on the floor wincing in pain. "Um..."

"I'm okay! Hey Fluttershy. Wanna chat?" Pinkie smiled.

Fluttershy rubbed one foreleg with the other. "Um...okay, I suppose I could use a buddy for support. I'm not feeling all that well."

"Aww, I'll do my best!" Pinkie said with a smile as she jumped up.

A while latere, AJ whistled as she washed her hooves in one of the bathroom area's sinks in the doorway, while Fluttershy nearby was squatting over one of the floor's squat toilets, with Pinkie to her side.

Fluttershy closed her eyes. "Okay...be the bat...be the bat...easy peasy lemon squeezy... Mmm, I think it's working, Pinkie."

Pinkie meanwhile was giving Fluttershy a back and flank massage. "That's the spirit! Go Fluttershy!" Pinkie pulled a foam finger from her underside, put it on her left hoof, and waved it around a moment.

Fluttershy cooed. "Oh, thanks. The comedy earlier helped too, hehe."

AJ chuckled as she dried her hooves with the air blower. "Well it's good you're feelin' alright now, sugarcube. I'll be figurin' out why this newfangled algae system wants to kill us."

Pinkie threw out the foam finger and returned to massaging Fluttershy's backside. "Probably Rarity's bad mojo." She blew a raspberry.

Fluttershy's rear made a similar noise, and she sighed in relief.

Pinkie giggled. "See, Fluttershy's rump agrees! Rarity's been a total meanie since we woke up. She didn't appreciate my jokes, and then just because I helped her wash up, she gave me a three bruises for it! I can hardly sit down or hug anypony now!"

AJ snorted. "There's cranky, and then there's bein' outright unfriendly, and we ain't got time or space for it right now. I'll have a li'l chat and try to untwist her britches. I don't care if there's still rocks in her head, she can't just go around bein' saltier than a hippogriff sailor who only comes ashore when the drinks are free and the fillies are half-off." She stomped out.

Fluttershy sighed. "Uh, you should go with her, Pinkie. I'm fine now, and the last thing we need is a fight..."

Pinkie gasped, stopping the massage to hug Fluttershy. "You're right! And...ow. On it!" She trotted on out.

A few minutes later, Fluttershy hummed a merry tune as she inspected the spider habitats between their bunks and the oxygen area.

Pinkie bounced over behind her. "Ooh, what task's this?"

Fluttershy sighed. "Just making sure our little pest-eating friends AJ brought are alright. It...looks like poor little Gerald here didn't make it."

Pinkie gasped. "Oh no, what did him in? Was it aliens? A bug mafia? An ALIEN bug mafia?"

Fluttershy blinked a moment, then brought the curled-up form of the spider up for inspection under a magnifying glass. "Um, just dehydration from a dry area of the enclosure, I think. Poor little guy, we could've saved him."

Pinkie put her ears down. "That's sad. Well, only one thing to do...plan a spider funeral!" She popped up with a sound of a party horn as confetti flew out every orifice and hopped into oxygen and around the corner. "I'll go get Applejack!"

Fluttershy blew a piece of confetti off her snout, and trotted out behind, heading across past oxygen and into comms around the opposite corner.

Twilight was sitting there deep in concentration.

Fluttershy knocked on the wall.

Twilight's ears perked up, and she turned around. "Yes?"

Fluttershy squeaked. "Um, sorry to bother you. Anything interesting?"

Twilight gulped. "We um... Look, don't freak out, but the link with Equestria went down shortly after we unpetrified, so I can't send any reports, and we may have an intruder aboard."

Fluttershy froze. "An...intruder?"

Twilight nodded. "Something...gooey and weird was on the outer hull. Celestia didn't catch it in the cameras until well after we were in petrosleep. Their best guess is it's Ocellus, since she went missing the day of the launch, and her dreams involve being a blob that can't maintain shapeshifts. About the only other likely possibility is the CMC did it somehow...they're in our storage somewhere, try to keep that one quiet around their sisters."

"Oh no. I hope they're all okay. Y-you don't think Ocellus got it in her head that because she's a changeling, she could fight these ones on her own, do you?" Fluttershy asked, shaking a little.

"That's Luna's working theory. At any rate, Luna's pretty sure she's okay, so we can worry about finding them and talking her out of whatever she's doing after the critical tasks are done. I'm sure she'd be useful fixing certain things."

Fluttershy nodded. "Alright, where am I needed?"

Twilight rubbed her chin. "Oxygen can always use another look-over, since none of us are really experts in growing algae, and it's the most critical. If that all looks okay...maybe check up on Rainbow. She was eager to see the cockpit and I'm a little worried she touched something. If there are no warning lights and everything matches what mission control has sent, we should be fine. I'm going to go find Spike and Rarity and make sure they aren't slacking off...you know how those two can get together."

Fluttershy giggled. "I do...it's pretty cute."

"Yeah yeah, but it's wasting time, and she's broken his heart before. I wouldn't be a good big sister if I didn't intervene..." Twilight said as she hurriedly trotted out.

Fluttershy went the other way, back the way she came, spotting Rarity looking out the observation window at the rust-red planet Marēs, and then turned to take a look at the massive green glowing tanks. All the status lights showed green. Fluttershy opened up a drawer and flipped open the basic manual, but was distracted as she heard what sounded like AJ and Dash arguing.

Suddenly there was a loud SLAP and Dash crying out.

Fluttershy peeked over one of the tanks. "Um, are you okay?"

Dash groaned as she rubbed her flank, which was bright red on one side. "Y-y-yeah...um...best of three? Ungh..."

AJ snorted as she trotted over Dash, giving a hard kick to the other cheek that turned it the same shade while smacking Rainbow into the wall. "I win, sugarcube. Now come along Pinkie, we got actual work to do now that that troublemaker's gotten a nice butt-kickin'. You know, Maud might want to know 'bout all these space rocks, and Twi said our comms are down..."

Pinkie sprung along as the two walked past Fluttershy.

Fluttershy went over to Dash. "Oh my...are you sure you're okay?"

Dash snorted loudly. "Yes, I'm sure. I'll get her back when me and her are alone. Maybe a nice prank when I call in a favor to get her on a date, after I can sit down again..."

Fluttershy put on a look of concern. "Um...I don't know if that's a good idea to trick a special somepony li-"

Rainbow jammed a hoof in Fluttershy's mouth. "Look, get off my case and back to your precious algae, okay." Dash stomped promptly into the cockpit, and shut the door behind herself.

Fluttershy sighed and went back to reading the manual. "Hmm, light levels are a little dim, probably just buildup...oh, the wiping cycle's stuck, of course! Let's see...a few things need power-cycling for sure..."

Within a few minutes, the efficiency meter on the algae returned to its normal 80%.

Fluttershy promptly smirked, and shook her rear around in a circle, doing a little dance. "No carbon dioxide buildup for us, hehe! All fresh as the forest, yippee! All thanks to lovely algae!" She repeated this a few times as somepony could be heard trotting towards, then quickly away from her, only stopping as she bumped into the cockpit door.

Rainbow's voice from inside the cockpit, sounding rather alarmed.

Fluttershy blinked, and put her ear against the door. "Huh? Rainbow, is somepony else in there?"

"Lightning, wait, you don't have t-" Rainbow shouted.

There was a sudden series of thuds.

Fluttershy gasped. "RAINBOW!" She immediately grabbed the manual door handle and tried to turn it, but it was stuck. She bashed with all her might, and it finally gave way...

A chair went flying across the room and onto the console. In front of Fluttershy, Rainbow's rear legs and tail were dangled from the overhead vent a moment before dropping down.

As Fluttershy put a hoof to Rainbow's side, preparing to turn her over, but noticing a distinct lack of wings or forelegs. She looked in the direction of a bit of rainbow mane well away from Rainbow's rear end...

She shrieked and slammed the alarm button next to the door.