Metroid: Mission P0N3

by LuluRainbow

Rating: teen
Tags: Death, Human, Main 6, My Little Pony: Friendship is Magic, Dark, Alternate Universe, Metroid, Starlight Glimmer, Original Character, Spike, Science Fiction, Adventure, Violence, Crossover
Length: 4293

Samus Aran is a lone bounty hunter who feels friendship is pointless, as she has had plenty of lone adventures over the years and has grown used to loneliness. A new mission, with 7 pastel ponies and a dragon, may just change her outlook on life.

(Metroid X My Little Pony: Friendship is Magic crossover fanfic, rated T since it is Metroid and darker themes will be introduced. This fanfic is most enjoyable if you have a decent knowledge of Metroid.)

(Tagged Human since Samus is technically a human.)

(Currently undecided where this takes place in the MLP "timeline", but it atleast takes place after Spike gains wings.)

Samus Aran, a lone bounty hunter, is sent to explore a distant planet with mysterious signs of life never before detected. On this planet, she finds 7 pastel ponies and a baby dragon. The mysterious beings, unsure of how they got there and how to return home, get wrapped up in Samus' greatest adventure ever. Can they get home and help Samus to see the power of friendship?

(This story is a sort-of passion project for me, as Metroid and My Little Pony are both things I really like and I wanted to try my hand at writing a crossover fic. As such I don't know how long this story will go on and am a bit unsure of where I wish to take the plot. I will try to update frequently, however!)

(The rights to Metroid and My Little Pony belong to Nintendo and Hasbro respectively)

Published 2020-12-06 08:20:01 UTC
Last updated 2020-12-13 03:59:57 UTC

Friendship...is Magic?

Twilight Sparkle and her friends had awaken from a slumber on a mysterious green and barren planet. Their memories were mostly intact, except their memories of what had led them here.

"So...what do we do?" questioned Starlight.

Twilight groaned and facehoofed.

"Does it look like I know?" snapped Twilight angrily.

Her friends gave her a shocked reaction.

"Sorry," she said in a softer tone.

"It's okay, Twi, it's not every day something like this happens," said Rainbow Dash.

"Yeah, this is even stranger than me!" said Pinkie as she bounced around.

The others sighed.

Just then, a giant orange spaceship landed on the planet. Out through the top came a bipedal cyborg-looking thing with reddish-orange armor, a greenish visor, and a gray arm cannon for its right hand.

Samus stepped onto the planet, looking at the 7 pastel ponies and their baby dragon with caution. The ponies and dragon stared back in disbelief and shock.

"Why hello Ms. Arm Cannon Cyborg!" shouted Pinkie

"Did...she just assume its gender?" questioned Applejack.

"Yes, she did," replied Rainbow.

Samus was shocked the creature could talk...and knew her gender. She took off her helmet, revealing a woman with blonde hair.

Applejack and Rainbow shot each other surprised glances.

"You...can talk?" asked Samus.

"Of course!" said Pinkie, as if it was a silly question.

"Ooookay," said Samus in a puzzled tone.

"And what exactly are you doing here?" she questioned them.

"Well you see, we don't actually know," said Twilight.

"Yeah! We kinda just ended up here and don't remember what happened just before that got us here!" exclaimed Pinkie.

Samus nodded, not sure what to make of this situation.

"You see, we're from Equestria, have you ever heard of it?" questioned Starlight.

"I can't say I have, and that's saying something as I've been to and have heard of many places," responded Samus.

"Bummer," said Rainbow.

"Yeah, Equestria is really cool! We have cupcakes and magic and friendship and-" Pinkie was cut off before she could finish her sentence.

"Friend...ship? Like...being friends?" questioned Samus in a puzzled tone.

"Why yes, darling. All 8 of us are very close friends. Don't you have any friends?" replied Rarity.

Samus sighed.

"I learned having friends has too many downsides. You lose them in the end, anyway, so it's better not to even be friends than to deal with the loss," Samus said sadly.

The ponies and Spike exchanged slightly sad glances for a second.

"That dragon of yours, is he hostile?" questioned Samus.

"I'm friendly, unless you get on my really bad side. Like being evil or something," replied Spike.

"Okay. I just haven't had good encounters with...dragons before," exclaimed Samus.

"So, what exactly do you do?" questioned Rainbow.

"I'm a galactic bounty hunter. I travel the universe, defeat evil, and all that fun stuff," she remarked sarcastically.

"Sounds exciting!" said Pinkie!

"Heh, I used to think that too," she responded solemnly.

An akward silence arose.

Samus continued the conversation.

"You see, I got a mission to come here and examine signs of life. It turns out you all are the signs of life that were detected," she said.

"Sounds like y'all have some fancy technology," said Applejack.

"You could say that," replied Samus.

"So, what are you going to do with us?" questioned Rainbow.

"I gotta bring you to a nearby research station. They'll examine you and stuff, try and learn about you," she responded.

The ponies and Spime looked slightly unnerved.

"Don't worry, it's not that bad," she started, "you'll be out of the research station before you know it."

"What happens after that?" asked Starlight.

Samus thought over the situation. She let out a slight sigh and responded.

"I guess you 8 can stay with me at my personal hub area. There will be rules to follow, and it is important you follow them. And as soon as we can find Equestria and a way to get you back there, you're gonna go straight home, got it?"

The ponies and Spike nodded in agreement.

"We haven't properly introduced yet! I'm Pinkie Pie! Just call me Pinkie though," exclaimed Pinkie.

Twilight smiled and began to talk.

"I'm Twilight Sparkle, but Twilight is fine! I'm actually the princess of friendship!"

"I'm Applejack, but 'ya can call me AJ," said Applejack.

"I'm Rainbow Dash! Rainbow or RD is fine, but only my close friends can call me Dashie," stated Rainbow.

"I'm Rarity, darling," stated Rarity.

"I'm Starlight Glimmer!" cheerfully explained Starlight.

"I'm Spike," said Spike as he pointed at himself.

"Hi, I'm Fluttershy," stated Fluttershy meekly as she waved.

"My name is Samus Aran, but most just call me Samus," said Samus.

She began to put back on her helmet as she spoke.

"We best be going. I think my spaceship should have enough room," stated Samus.

"Oh goody! A real alien spaceship! I can't wait to see what kind of tech you have! Is that a genuine arm cannon on your arm?" Pinkie questioned.

"Yes," sighed Samus, "and don't you dare push any buttons in my spaceship! It's dangerous for untrained people-well I guess ponies and dragons in this situation."

Arrival at the Research Lab

It didn't take long for the group to arrive at the Biology & Zoology Research Laboratory. Samus was greeted by several scientists once she had arrived.

"I have brought the lifeforms from planet E-QUINE. They are indeed passive and act very friendly, and can even...talk," stated Samus.

The scientists stared in shock at the pastel-colored creatures and the purple drsgon and began taking notes on them.

"We will keep them for examination for a few hours," stated one scientist, "and it will be up to you what to do with them afterwards."

Another scientist approached Samus.

"The scientists other at the other laboratory have figured out a way to get their abilities back from your suit after powering it down. This will allow you to power down after missions but keep your abilities. I think they said it uses some form of the cloud, but that's jot my specialty," he shrugged before continuing, "I suggest you go there while we conduct our research on these new creatures."

Samus nodded in agreement, "Sounds like a plan."

Samus gave one last glance towards the ponies before her departure.

On her way to the Technology Research Laboratory, she gave more thought about the new pony-like creatures she had encountered. Was the purple one, Twilight, actually a princess? How could one be a princess...of friendship?

Upon arrival to the laboratory, she found it mysteriously empty and seemingly devoid of any life. A "CAUTION" sign sat haphazardly placed on the entrance doors. Samus opened the entrance door, as it was unlocked, and stepped inside. Everything seemed to be normal, except the lack of people. Straight ahead sat the computer, with all of her upgrades listed.

Samus shrugged, "I think this is relatively easy to handle on my own. It just needs to transfer the data to my arm cannon."

Samus pressed the transfer button.

TRANSFER LOCK REMOVED, PREPARING FOR DATA TRANSFER

Just then an alarm sounded.

"What the...?", questioned Samus to herself.

DANGER: EQUIPMENT ON THIS MACHINERY IS MALFUNCTIONING. IT IS UNSAFE TO REMAIN IN THIS AREA. EVACUATE AS SWIFTLY AS YOU CAN!

As Samus turned around to head straight back through the entrance, part of the ceiling above it collapsed into a pile of rubble. Samus shook her head.

"Couldn't ever be easy or convenient, huh?" she muttered to herself as she scanned her surroundings. She jumped on top of the rubble and entered a higher floor of the laboratory. She saw an "Emergency Escape" hatch on the opposite side of the room from her, but there was one issue.

The room was filled with smoke and fire, making it a risky endeavor to traverse the room. With some strategic rolls around fire and some crawling, she finally made it to the other side, opened the hatch, and looked down.

It was a narrow path on the side of the laboratory that led back to the front. Samus hesitated a bit, but one look back at the blazing fire behind her was enough motivation. She jumped and grabbed the narrow ledge, letting out a sigh of relief.

She pulled herself up and sidled across the ledge to the front. By now the laboratory was ignited in flames all over, and Samus rushed to her spaceship.

Mere seconds after she had taken off, the laboratory exploded behind me.

"Great, there goes any last chance of recovering all my upgrades," Samus grumbled to herself.

With this pseudo mission a failure, it was time to return and check on the researcher's progress. Samus let out a chuckle.

"Hanging out with those ponies might not be so bad afterall, a lot better than near-death experiences at least. Though I do wonder how they even ended up on a random planet in this great and wide galaxy, and where this Equestria they speak of is..."

Samus had so many questions and yet so few answers.

Author's Note

Can't have Metroid without an escape sequence towards the beginning!

A Galactic Home

Soon after barely escaping death's grasp, Samus arrived back to the Biology & Zoology Research Lab safely. Upon arrival, she told a few of the scientists of her experience.

"Sounds like the machine was rigged to me, like some kind of death trap," said one of the scientists. She stood out among the rest of the scientists, as she wore a black coat with black-tinted glasses.

"Who are you?" asked Samus. The woman looked out of place there.

"Who, me?" the woman asked, seemingly faking ignorance.

"Yeah. I haven't seen you before, and you dress...differently from most scientists I've seen," Samus replied. This woman did not give her good vibes at all.

"Heh. I'm just a new recruit here, you could say. You can call me...Lyrid," she answered with a disturbing grin before she walked away.

Samus stood there for a few moments, thinking about Lyrid. None of the scientists there really had technological experience, and a death trap was a very odd assumption to come to when it very well could of have been a machine malfunction.

Her thoughts were disturbed by another scientist.

"Well, Samus," he started, "we have learned little about these new creatures we have discovered, besides the fact they are indeed ponies and a dragon.. They show up as originating from Equestria, and we can't find any matches within millions of light years. We'll keep up the search, but for now we can do nothing. We suggest you bring them back to your place for now, and keep them safe."

Samus nodded as the ponies and Spike walked out of the testing room.

"Hey, Sammy!" greeted Pinkie cheerfully as she bounced towards Samus.

"Don't call me that," muttered Samus.

"She must be fun at parties," Rainbow whispered to Twilight.

"Well, you don't appreciate being called Dashie randomly, do you?" accused Applejack.

Rainbow groaned.

"Come on, you eight, let's get back to my personal galactic hub. I need a bit of relaxation after all this excitement," Samus told them.

"Okie dokie lokie pokie!" agreed Pinkie with a giggle.

They entered Samus' spaceship, and Samus started off.

"So, you're the Princess of Friendship, Twilight?" she questioned.

"Yep! You see, alicorns are very important in Equestria. There are currently only 5 alicorns alive!" Twilight exclaimed, trying not to sound like a nerd.

"Alicorn? Like a unicorn with wings, like you?" Samus questioned, quite confused and interested by these creatures.

"Mhm!" answered Twilight.

"I've heard of and seen some strange creatures before, but you eight take the cake," Samus said with a very weak chuckle.

"CAKE!? WHERE?" questioned Pinkie.

The other ponies facehoofed and Samus shook her head.

"What?" Pinkie questioned while shrugging.

Just then, they landed at Samus' personal galactic hub. Getting out of the spaceship and entering inside, the ponies and Spike were amazed by the layout of the place. A big huge couch close to a massive television particularly interested them.

"What's this?" Applejack asked as she pointed to the television.

"You don't have televisions in Equestria?" Samus asked, very surprised.

"Nope," replied Applejack.

"I think I heard of them once!" exclaimed Pinkie.

"You have?" asked Fluttershy.

"Yeah, Discord let me burrow his book about Marvelous Mankind Machinery!" Pinkie stated nonchalantly before gasping.

"I never returned it before we ended up here! Discord's not gonna be happy!"

Samus stared confused before asking a question.

"Who's Discord?"

Pinkie giggled.

"Discord was this mean scary chaos monster lord who can do anything at the snap of a finger! He took over Equestria and turned us against each other, but the power of friendship prevailed and turned him to stone! But then one day Celestia, the alicorn ruler of Equestria, asked us to reform him! And with the help of our friend Fluttershy he's good now! Except for that time with Tirek, Tirek was this big scary magic-stealing cent-"

Pinkie was cut off by Twilight.

"You don't have to go into those details, Pinkie," Twilight said whilst rolling her eye.

Samus looked amused.

"You didn't tell me you actually fight evil! Maybe I should take you eight on a mission sometime, would make my job a bit easier. Not that I need any help, to be honest," Samus said as she took off her helmet and grinned.

Twilight stepped forward.

"Are you sure about that?" she questioned to Samus.

"Yes, very sure," replied Samus.

An akward silence arose.

"Well, I'm gonna take a shower, you eight help yourselves to something in the kitchen. I don't know what you all eat," Samus shrugged.

Pinkie smiled, and music started out of nowhere.

"She isn't..." facehoofed Rainbow.

"She is," Starlight replied with a sigh.

"Is she about to sing about food?" questioned Samus.

"Yep," answered Applejack.

"Everypony loves a bite to eat,
We crave sugars and sweets,
At the table we will take a seat,
We just won't eat any meat!"

Pinkie began bouncing across the room

"Apples, oranges, tomatoes,
Bread, wheat, even pie,
Carrots and potatoes,
Onions we'll even try!"

"Did she say...pie?" questioned Rainbow.

"Yep," nodded Twilight.

"Cupcakes and cake,
Any tasty treat,
Your oven can make,
And every single sweet!"

"Pinkie, I think that's enough," said Spike.

"Awww...two more verses, please?" Pinkie pleaded with sad eyes.

"Fine," said Spike.

"Oats, grapes and saltines,
Pumpkins, pears,
Gravy and green beans,
We're not picky mares!"

"We're not all mares, grumbled Spike.

"And now you know,
A lot we will eat,
That is so,
Just not meeeaaatttt!!!!!"

Pinkie giggled.

"Al...right, I'm gonna go take that shower. Enjoy all those foods, I guess," Samus said with a shrug as she walked to the bathroom.

Pinkie looked around, "was it too much?"

"Kinda, maybe, yes," responded Fluttershy.

Pinkie shrugged and giggled, "I liked it! Now let's see if we can watch something on this television! The cool kids call it a TV, ya know!"

Author's Note

I can't say too much, but Lyrid will be an important character and might have some relation to an iconic Metroid character ;)

Had to have Pinkie sing a kinda cheesy and silly song.

EMERGENCY MEETING

It had all happened relatively quickly for Samus. She had been sleeping before being woken up by an emergency alarm. She had rushed to get her suit on and leave, having practically avoided the questions of the ponies. Now she was talking to top security officials of the galaxy.

"I came as quick as I could," Samus said.

One of them nodded.

"Very good. Our situation, however, is not," he sighed.

"You see," another man began, "someone broke into the DNA Storage Hub."

Samus gasped.

"What did they steal?" she questioned.

"They stole everything and burned the place to the ground," he replied.

"Weren't there DNA samples there that could potentially be used to recreate...metroids?" she questioned.

"Yes," replied a familiar voice.

Samus looked around and spotted a familiar black-haired woman.

Lyrid.

Samus locked her eys on Lyrid, shocked and confused by her precense here.

"You, I've seen you before," stated Samus.

"You...have?" questioned Lyrid with a sly grin.

Samus stepped forward.

"What do you know that I don't?" Samus questioned, sounding slightly annoyed.

Lyrid shrugged.

"I don't know what you mean, sorry. Oh, what is that behind you?" she questioned.

Samus looked behind her to see nothing. Suddenly she heard an noise that sounded like an explosion as smoke filled the room.

"Emergency! It's an emergency! Evacuate this place immediately!" screamed a man from the top floor.

Samus looked around and spotted Lyrid running off.

"Not this time," Samus muttered to herself as she chased after her.

Samus could barely see in front of her, but she continued to follow the sound of footsteps. The hallways felt long and endless, and she was starting to run out of breath.

She stopped for a second and looked around. She could know smell flames burning, and the far-off footsteps were now hard to track down.

She looked up and saw a small vent she could crawl through. With a well-timed jump she grabbed the ledge and crawled in. She was glad the vent was big enought to crawl through instead of having to use her Morph Ball she no longer had.

Before long she jumped down in a new room. Her suit began giving her a temperature warning, indicating the room was very hot. In front of her stood Lyrid, however.

Samus prepared her arm cannon, and was ready to shoot befoe Lyrid interrupted you.

"Do you really think you can use that puny little...pea shooter to defeat me?" she asked with a laugh.

Samus fired a few shots, and Lyrid dodged them easily.

Lyrid immediately retaliated and rushed towards Samus, pinning her to the wall.

"I could kill you right now, but that would be no fun. Instead, I'll just leave you here. Give you a slow and painless death. Really is a shame that the great bounty hunter Samus Aran is gonna kick the bucket this way, isn't it?" mocked Lyrid.

Lyrid let go of Samus and stepped back, and Samus collapsed to the ground. She pulled out a mysterious device and disappeared in a puff of smoke.

Samus tried to stand up, but quickly began to slip from a conscious state.

"Not this...way," she groaned. It seemed the heat was destined to kill her. Even if it didn't, the flames around the room surely would.

In a poof of purple-hued magic, it seemed that the purple alicorn from before had appeared. Samus passed out, that her last vision. She had prayed to any gods above that she would wake up.

Author's Note

Kinda ended this chapter on a cliffhanger, but you know what will happen. Maybe Samus really was lucky to have met these ponies!

Awakening

Samus' eyes opened. She looked around, noticing she was back at her personal hub and surrounded by the pastel ponies. They had somehow saved her and even had removed her Power Suit, allowing her a safe and comfortable rest. She looked towards Twilight Sparkle and spoke.

"What was that? Did you-" she couldn't finish her sentence.

"Yeah, she saved you," replied Rainbow in a slightly frustrated tone, sensing Samus was trying to keep her ego intact.

Samus sighed.

"I didn't need a pastel-colored horse, I could've managed by myself!" Samus exclaimed.

Twilight furrowed her brow before speaking.

"She sure about that? That woman had you nearly-"

"I was fine!" Samus retorted, practically yelling.

Twilight flinched, before glancing over at her friends. They all shared shocked glances.

Samus groaned and began to speak again.

"It's fine, I suppose, but don't you ever pull a stunt like that again," she demanded.

"Look, lady, Twilight Sparkle saved you whether or not you want to admit it! Is that how you treat somepony who saved your life?" Rainbow questioned to Samus with an angry glare.

Samus stood up from her bed and sighed.

"I don't have time for this. You all stay here from now on, no matter what happens to me. Got it?" she asked in a slightly booming voice.

The ponies and dragon responded only by nodding as Samus equipped her suit.

"W-where are you going?" questioned Fluttershy meekly.

"I'm gonna show that little scientist piece of crap what happens when you mess with the greatest space bounty hunter, Samus Aran," she stated as she entered her spaceship.

She was off before any of the ponies could argue against it. Twilight shook her head.

"That scientist, she isn't a normal human being. She has this magical device that can teleport her, but she seems to have powers beyond that. I assume super strength is one of them. She sort of reminds me of Discord a bit, but I don't know if her powers are that great," she stated.

"How does Samus intend to survive another encounter with her, then?" questioned Rarity.

Twilight began to pace around the room and think, before suddenly stopping.

"A-ha!" exclaimed Twilight.

"You got it? I mean, you got it! ...right?" asked Pinkie.

"Indeed I do, Pinkie. I remember Samus saying before that her suit could be upgraded with special abilities. If she had every ability she could find, she might actually be able to win against this scientist who can seemingly easily kill her," stated Twilight.

"Uh, Twilight, how do we get her these abilities?" Applejack questioned.

"Oh, right. Well, I snuck a few of Samus' books about that supercomputer she has over there. If we do a bit of code inputting, we may be able to track down the upgrades to an extent," Twilight finished with a smile.

Rainbow grabbed a space helmet with her wing and equipped it.

"Whatcha doing, Dashie?" Pinkie questioned.

"I'm gonna stop Samus and tell her our plan. Ego or not, what she is doing is stupid. You all work on tracking down those upgrades. I'll be back shortly," Rainbow stated.

Her friends wished her good luck and began work on locating where Samus could regain her abilities.

It seemed like everything was going good. Samus would get the upgrades, the evil scientist would be defeated, and the ponies would find a way to return home.

Little did they know their long and dangerous mission was just beginning.

Author's Note

Things are about to kick into full gear! Before long Samus will be tearing down enemies and discovering upgrades!

EMERGENCY TRANSMISSION

Samus had just returned from a long and dangerous mission, and was ready to get a bit of peace. Not that she could get much of that anymore. She powered down her suit, as per protocol, which she had learned to hate. It meant every mission she had to rediscover her abilities, as such were the pains of being a galactic bounty hunter.

Just then, an emergency siren sounded and the nearby screen filled with text. A robotic voice read a emergency transmission. Samus sighed.

"Darn it," she sighed.

EMERGENCY TRANSMISSION

AN UNKNOWN FORM OF LIFE HAS BEEN DETECTED ON PLANET E-QUINE. THERE APPEARS TO BE TWO NEW SPECIES LIVING ON THIS PLANET, AND BY SCANS OF THE PLANET'S BIOLOGY WE HAVE DEDUCED THEY ARE NOT RELATED TO ANY SPECIES OF METROID. IT IS YOUR JOB TO CONTAIN THEM AND BRING THEM BACK SAFELY TO ANY NEARBY RESEARCH LAB. THESE BEINGS ARE ASSUMED NON-HOSTILE, ONLY ATTACK BACK IF OBSOLUTELY REQUIRED. IS YOUR OBJECTIVE CLEAR?

"Yeah, yeah," grumbled Samus. One of these days she was going to be given a dangerous mission, with none of her former equipment to help her.

She pressed a nearby red button to open the space ship garage that was built into her personal hub. She entered her spaceship and set a course for planet E-Quine, curious of the new beings she might discover there.

Lyrid's Mission

Lyrid walked into her personal laboratory, dimly lit by her computer screen. She sat down in her computer chair and opened up a chat program. She saw one message.

"Do you have the results?"

Her boss had assigned her to retrieve the documents detailing the pastel ponies and their dragon, which she had accomplished. She typed out a response.

"Yes."

She sat back and grinned as she awaited a response.

"Good. The fact that the bounty hunter survived the trap is a slight hindrance to our plans, but we can figure out something."

Lyrid skimmed through some of the pages. It appeared to detail some of the ponies' strengths and even weaknesses, which piqued her interest. Another message popped up.

"I think we should initiate Plan #388."

Lyrid paused. Plan 388.

She quickly typed out a response.

"Don't you think that plan is a bit extreme?"

She was quickly met with an answer.

"You may have their strengths and weaknesses right with you, but I know the power those ponies can have. And you surely know how powerful Samus can become. This is the only way."

Lyrid sighed and typed some more.

"Fine."

She was met with another response.

"Burn the place down after you get the DNA samples."

Lyrid had one last question she typed out.

"Isn't the place swarming with guards and all that?"

Another quick response.

"I took care of that, trust me. Just go."

Lyrid sighed and stood up. Surely those pastel ponies couldn't be that big of a threat.

She opened her door and left the room.

Author's Note

I didn't forget this, don't worry! Anyway, I want to have more short chapters like this with Lyrid. I want to explore more of her character and the mystery of who her boss is.
Plus this chapter will help move the plot forward.