Metroid: A Hunter in Equestria

by Cusi

Hunted Hunter

Disclaimer: Samus and Metroid elements belong to Nintendo. My Little Pony belongs to Hasbro/the Hub. I own nothing but the plot.
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Twilight, Spike, and Zecora were galloping away from the library, where the Element of Magic was located before Twilight picked it up. The golden tiara was now resting on the mare's head. They were now heading toward the road to Whitetail Woods, where apparently Samus awaited. They almost reached the town outskirts when a voice suddenly spoke and stopped them.

"Hold it right there!" an azure unicorn mare exclaimed. "Trixie has finally found you, Twilight."

"Trixie?" asked Twilight. "What are you doing here?"

"Trixie has come to challenge you to a duel." declared Trixie. Twilight frowned and attempted to rush past Trixie, but a magical tug on her tail stopped her. "Trixie will not take 'no' for an answer."

"I don't have time for this. Whatever you want, it'll have to wait." said Twilight in an almost angry tone.

"Go away, Trixie. This is more important than some stupid grudge of yours," angrily shouted Spike. He threw a dirty glance at the showmare. Zecora simply frowned at Trixie's actions.

"Ha! What could be so important that you have to make Trixie wait? Surely it can't-" Trixie was interrupted by Twilight, who put her face just an inch away from showmare's. Twilight wore a scowl on her features that made Trixie stop talking as she moved her head back a little, taken aback by the sudden intensity of Twilight's glare.

"My friends have been captured by someone with devastating power and unknown intentions. If I don't face her and defeat her, she'll probably do unspeakable things to my friends; and that's assuming they're still alive." She shoved a hoof at Trixie's chest. "So unless you are here to help, I suggest you get lost and stay out of my way."

Twilight ran past Trixie and continued her way to Whitetail Woods' direction. Zecora and Spike followed soon after, leaving Trixie behind.

The showmare watched them go with a stunned face. Her face quickly contorted into an intense scowl. She growled and slammed the ground with her forelegs several times. Her anger quickly diminished and she calmed down, though she was still angry. "So that's what those explosions were..." Trixie then turned around and galloped back to her wagon. "Curse you, Twilight." she said under her breath.

Unbeknown to the showmare, a certain dust-colored earth pony stallion saw her gallop away. He put his hoof on his chin in contemplation, until he decided to follow her, making sure to stay out of her sight.

A hawk was flying over the edge of Ponyville. It kept its gaze on the ground, looking for its targets. So far, his search has proven fruitless. The bird was about to give up and return when a single metallic corner became visible through the trees. The hawk cawed and went to investigate.

There, just on the edge of the Everfree Forest, a cage holding five ponies was visible. The hawk landed on a nearby branch and screeched loudly, catching the attention of four of the five mares; the one with rainbow mane was still unconscious. It regarded the ponies with sharp eyes before it took to the air once again. The hawk then proceeded to fly around in circles in the space above the cage, loudly screeching every now and then.

"What's with the bird, Fluttershy?" asked Applejack.

"I don't know. I've never seen him before." responded the yellow pegasus. "He seems to be calling for someone, though."

"That would be me." said a light blue -almost white- pegasus with a slightly darker mane styled in a ponytail. Her eyes were a cobalt color and her cutie mark was that of two generic-looking clouds.

"Who are you? I've never met you before, so you're not from Ponyville. Where are you from?" asked the hyperactive pink mare.

"I'm Misty Breeze and this is Looker." said the new arrival as the hawk perched itself on her back and screeched. "I've come to help you."

She was about to kick the cage's door when Rarity yelled at her. "DON'T TOUCH THAT CAGE!" Taken aback, Misty Breeze asked why. "It's electrified. To keep others away." Rarity added.

"Huh. Guess I won't be of much help, then." Misty Breeze lowered her legs and frowned. She quickly perked up. "That's ok, though. Wait here and I'll bring someone who can."

"Wait!" said Applejack. "How did you find us?"

"That was Looker. I just followed his lead." Misty Breeze answered.

"No. Ah mean how did you know we needed help?"

Misty looked down for a bit. "I'm aware of the situation you're in. I can't say more." She quickly lit up and smiled. "Don't worry. Just know that you are not alone." She turned around and galloped away, Looker flying just above her.

"Wait! You didn't tell me where you're from!" yelled Pinkie Pie, but the mare was gone.

Samus sat on the ground after launching those missiles to lure Twilight. She had her Power Suit on, and was browsing through her logbook to pass the time. She was re-reading her notes about her metroid DNA and her apparent ability to drain energy. Why it only seemed to work when her suit was on was what had her thinking. She kept pondering for a while until a message on her visor snapped her out of it.

"Spatial anomaly detected."

Before she could look for more information, another message flashed.

"Spatial anomaly no longer detected."

"That's weird." Samus said to herself. She tried activating several sensors on her suit, and even asked Adam to run a scan from her ship, but everything proved useless. She would have to make a more throughout investigation later.

"I'm here." Twilight's voice brought Samus out of her pondering. "Let's end this."

"Let's make this right. I'm at your side, Twilight." Zecora said as she took place beside Twilight.

Spike took the other side, but said nothing. He just gave Samus a look full of both determination and sadness; something the huntress took notice of.

"Why did you bring him?" Samus asked angrily. "This was between you and me."

"It was his choice." answered Twilight. "He's come to see this end." Spike just nodded in confirmation.

Samus looked at the dragon again. She seemed to be mentally debating something, until she gave one nod, as if understanding what had to be done.

"Very well." said Samus in a sad tone. "I'm sorry, Spike. I really hoped you would've stayed behind." She raised her cannon and aimed it at the trio.

"Why?" asked the baby dragon as he looked intently at Samus's eyes behind the helmet. "I thought we were your friends. I thought I was your friend."

Samus hesitated. She lowered her cannon for a moment and looked directly at Spike. For the briefest of moments, a baby metroid stood in his place. One blink and he back to being a dragon. Several memories coursed through her head, all involving her baby; the most prominent one being when she saw the egg hatch, releasing a cute little fanged jellyfish. She remembered seeing the baby float around her in curiosity and, dare she say it, love toward her.

She closed her eyes and reminded herself of the present. She opened them and began speaking. "It's personal." She pondered for another moment, and then looked at Twilight. "You said you would do anything to have him safe and sound at your side; that you'd pay any price. Well, I'm paying the price now." She raised her cannon once more and opened fire.

Land Scout carefully trekked behind some bushes. He was following an azure coated unicorn mare, though the fact that she was galloping at full speed and that he wanted to stay out of her sight made it difficult for him. But never be said he lost track of something. Always keeping himself on track was, after all, his special talent.

The mare eventually reached her wagon, from where she produced a chest. Land Scout watched as Trixie picked up one specific outfit and donned it on herself. The stallion could barely contain his glee as he watched the mare dress up and gallop away. Once the mare was gone, he emerged from his hiding spot and almost laughed manically.

"I knew it! Ahahaha! I knew it!" He pumped a hoof in the air. "I flying-featherly knew it! Dang it, Land Scout, no one beats you in tracking! Who's the best? You're the best! Ahahahaha!"

His self-celebration paused when he heard a far-away screech. He looked up to the sky and saw Looker flying around something. It didn't take long for him to realize the hawk had found something. Land Scout wasted no more time and rushed to see what his feathered friend had found. His grin never left his face, though.

On his way, he saw Looker fly down. A few minutes later, the hawk had taken flight once again, this time heading towards him. He put a hoof on his mouth and whistled loudly. The sound caught the hawk's attention and it changed its course to land on Land Scout's back. He looked at the hawk and petted it.

"Fancy meeting you here. What are you doing?" asked a light blue pegasus mare. She had come from the same direction Looker came.

"Oh, Misty! I wasn't aware that you would be here. Are you back-up?"

"I was about to ask you the same question." replied Misty Breeze. "Why are you grinning like an idiot?"

"Oh! I have just confirmed my hunch! All I have to do-"

"Yeah, yeah. Congrats, and whatever." Misty's face went from teasing to serious. "I actually need your help."

Land Scout finally stopped smiling after looking at her face. "What's wrong?"

"Turns out the would-be newbie went rogue."

"The would-be new... Samus?" Land Scout leaned closer, curiosity drowning his earlier glee. "What do you mean by rogue?"

"Yeah, her. She came to the castle yesterday and incapacitated almost a hundred guards in less than an hour. She stole the Elements and is now hunting down their bearers."

"WHAT?!" Land Scout yelled. He was beyond flabbergasted. "Why would she do that?"

"No one knows. And there's more. She said if either Celestia or the Royal Guard interferes, she'll bomb Ponyville and everypony within it. The worst part is she already captured five of the Elements."

"Is that why you're here?"

"Yeah. Luna and I came to offer support. My task is to find and help the Elements. Luna went ahead to search for Samus's ship and neutralize it. I already found the Elements, but Samus turned more cautious than expected." Misty said while glancing at the general direction of the bearers.

"How so?" Land Scout inquired.

"She electrified the cage they're in. Contact will result in a nasty shock."

"Darn. Hmm..." Land Scout immediately lit up. "Well, then it's good that I just happen to find the mare that will help us."

Misty gasped. "You don't mean..."

"Yup! I finally found her! Come on, let's go get her. She headed to where the five blasts came from."

Land Scout and Misty Breeze dashed, Looker flying behind them. They ran past trees, following the signal Samus had sent a while ago. Even with the news he just received, Land Scout couldn't help but smile at his success.

Twilight erected another barrier as a missile made its way toward her. The blast impacted on her shield, but made no real damage to the mare. She looked around and spotted Zecora with some soot marks and panting heavily. The zebra jumped and another missile exploded on the spot she was in. The unicorn redirected her attention to the armored human and shot a bolt of magic at her.

Samus sidestepped effortlessly as another magic bolt sailed by her. She raised her cannon to return fire, but quickly jumped to her side as a green fireball attempted to strike her. Before she could even aim, Zecora tried to ram her. Samus deflected her with a kick, but didn't press on because she avoided another magic bolt.

The Hunter was getting tired of wasting time. She thrust her arm at Twilight and her Grapple Beam shot out from the round jewel in her hand, quickly attaching itself on the mare's horn. Twilight screamed when Samus began swinging her. Once enough momentum was acquired, Samus used Twilight as a wrecking ball and slammed her onto both Spike and Zecora.

The zebra and baby dragon didn't land far, but they were clearly in pain. Samus pulled Twilight toward her and stopped the mare with her foot. Samus then pushed Twilight to the ground and pressed, immobilizing the unicorn. Without missing a beat, she fired an Ice Missile at Zecora and Spike, freezing them on the spot. Once they were neutralized, Samus put her attention on the unicorn under her boot.

"You lose." Samus said ominously. "Powerful as you may be, combat is really not your strong suit."

Twilight said nothing, instead giving the huntress an almost hateful look. The Grapple Beam retracted, and Samus charged her Wave Taser. She moved to tase the lavender unicorn, but a powerful pink bolt hit her side and sent her flying. A second later, a pink fire snake rushed toward the frozen pair, melting the ice and thawing its victims out.

"Rise, Twilight. You won't fall today, not here." said a voice belonging to a mare.

"Why does everyone keep interfering?" Samus asked with venom on her voice. She got up and took a look at her attacker. She was a unicorn mare donning a full-body silver suit that covered every part of her body, including her face. The mare was wearing a white hood and cape above the suit, as well as a black mask covering her face. A pair of small rubies adorned her forelegs. "Who are you supposed to be?"

"You can call me 'Silvermane'. I'll be your opponent now." 'Silvermane' said. She turned to Twilight, who was looking at her with awe and gratitude. "Go! Find your friends and go look for someplace safe. I'll deal with this thing." said Silvermane as she put her attention back on Samus.

"Thank you." said Twilight. Spike and Zecora quickly joined their friend, bowing their heads in thanks. They were about to run back to Ponyville when another two ponies joined the party. One was a dust-colored earth pony stallion and the other was light pale blue pegasus mare. The stallion looked surprised for a second, but quickly recovered.

"That works, too. Come on, Miss Sparkle." Land Scout said as soon as he saw the lavender mare. Silvermane shot her a dirty look when she heard Twilight's last name. "We know where your friends are being held!"

"Follow us!" Misty Breeze exclaimed. Twilight, Zecora, and Spike began following the newcomers.

"I don't think so." Samus shot a Super Missile at the fleeing party.

"I think so." The Super Missile glowed the same pink as Silvermane's magic and stopped moving. It quickly spun around and flew toward Samus. "Don't waste anymore time. GO!"

Samus, for her part, cursed loudly as her body was sent flying from the blast of her own attack. She gave another look at Silvermane; she wouldn't catch her prey as long as the unicorn was there. Missiles were also out, unless she wanted to get blasted by her own weapons. She looked around and saw several Twilights, followed by several clones of her friends, running away in different directions. "What's going on?" She switched to the X-Ray Visor and saw only silhouettes. All of them managed to get away, so she reverted to the Combat Visor.

"Illusions." the masked hero responded. "Not to brag, but I'm quite good at them."

Furious as she should be, Samus couldn't help but chuckle. "Well, this is certainly going to be interesting."

"I wholeheartedly agree." Silvermane's horn began glowing again.

Samus tensed, waiting for anything that could get thrown her way. She stood still for a moment, until she began feeling very heavy. It became increasingly difficult for the Hunter to stay standing, and she eventually fell to her knees. She turned to Silvermane, who sported a victorious smirk, even if it was hiding behind her mask.

Samus eventually realized what was happening. A second later, the metallic orange in her suit changed to a shiny purple, and she no longer felt heavy. She easily got back to her feet. This brought a satisfying reaction of surprise from the masked mare.

"But how?! What did you do?"

"The Gravity Suit nullifies any adverse gravitational effects. I would never have expected gravity manipulation, though." Samus commented casually.

"I'm still working on it." Silvermane said as she stopped her gravity spell. "Though it looks like it works quite well."

Samus nodded once, then let loose a barrage of Plasma shots. Silvermane jumped back and evaded the shots. She responded with another bolt of magic. This bolt however, was thinner and faster than the one shot before, resembling those of the Plasma Beam. Samus had a hard time evading it.

"Beams instead of bolts?" Samus asked.

"I'm good at mimicking. Check this out." Silvermane's horn glowed once more. The pink hue began to solidify into a cylinder of sorts. A few more seconds and the hue took on the form of a Super Missile. Silvermane then hurled it toward Samus, who had to jump again to avoid most of the damage when it exploded with as much ferocity as a real Super Missile. "So what do you think?"

Samus looked at the mare with surprise. She quickly recovered. "I'm done playing."

"And I'm just starting." Silvermane's hooves began glowing pink. Then she started gliding around Samus, as if she were skating.

As the mare glided around the huntress, several clones started to form where Silvermane's body passed, as if leaving afterimages. Before long, four Silvermanes were gliding around Samus. Something about this particular strategy just irked Samus.

"I usually don't like clichés, but I can't help but ask: Which one is the real one?" all four Silvermanes asked simultaneously.

Samus immediately switched to her X-Ray Visor. She saw four silhouettes moving around her, but only one of them had a visible skeleton. "That one." She took aim, but before she could fire, a magic beam hit her from behind.

"Wrong." they all said at the same time. "The correct answered is: All of us." As soon as they finished their response, all four Silvermanes began shooting Samus with their beams. Samus, now knowing what to expect, evaded all the bolts fires her way, though she couldn't find enough time to counterattack. She prepared a Charge Shot just in case.

"Clones?" Samus asked as she leapt to her side, nearly getting hit by a beam aimed at her head. On that split second, she locked on the skeletal image and fired her weapon. The gliding unicorn couldn't avoid the blast and got hit dead on. The force of the blast still sent her spiraling through the air, so Samus quickly switched to the Plasma Beam and incinerated the rest of the gliding annoyances. Or at least it looked like it, since they burst into pink fire once the red beam hit them.

"Not quite." answered Silvermane as she struggled to stand up. "They are certainly more than mere illusions, but they aren't really clones. They're more like..." She left the sentence hanging, not knowing what to say.

"Echoes." Samus finished for her. Now she knew why the mare's previous strategy irked her.

"Hmm... Yes, I like how that sounds. They're echoes." Despite the bad shape the mare's suit was in and the heavy breaths, Silvermane managed to sound quite pleased. "Thanks for the name."

Samus regarded the mare for a few moments. "You look tired."

Silvermane didn't take her eyes of the huntress. Her horn glowed a little, but the light flickered. "And you look fresh and ready to keep going. Mind telling me your secret?" she asked with heavy breaths.

"It's all thanks to my Power Suit. But unfortunately for you..." Samus activated the Diffusion feature of her beam weapons and charged. "... I can't waste any more time."

Samus released the shot just as her Arm Cannon glowed pink and it rapidly moved to her chest, making the Hunter effectively shoot herself. The powerful beam exploded on the Power Suit, causing massive damage and sending Samus flying through a tree.

Silvermane saw the result of her plan and gave a big sigh of relief. She let herself fall on the ground and rest for a little while. "Thank Luna it's over. I don't think I would've lasted much longer."

Samus groaned and got up. She had seen her beam deal extensive damage, but in all her years she had never experienced in firsthand. She walked toward the masked mare, who got up as soon as she saw her. Samus was now angry, and her pride had suffered a big blow by shooting herself. The huntress ran at the mare with the intent of pummeling her.

"HIYAAAA!"

Samus found herself in the air again. She landed a couple of yards away with a crash. Ok, this time she was careless. "Martial arts, too?" Samus asked as she got up.

"I'm a mare of many talents." was Silvermane's smug reply.

Samus was still angry, but that maneuver had reminded her that she had to keep calm. She approached the masked mare again, but this time it was with calm and even steps. Screw what the voice in her head said, leaving this mare alive would prove too risky. She configured her cannon on the Imperialist, the Kriken sniper weapon, as the linings in her Arm Cannon colored red.

Silvermane noticed the change and charged her horn. She let out a blinding flash, buying some time as the Hunter recoiled a bit. She jumped out of the way as a red laser passed by the place her head was in, piercing everything in its path. She wasted no more time and her horn glowed a bright pink again. While she charged her spell, she kept moving to avoid being pierced by the Hunter's sniping laser; her movements random as to avoid revealing patterns.

Samus, for her part, had difficulty aiming. The mare was moving too much and in erratic manners, not to mention her cape was misguiding and distracting. She fired several shots, but they did nothing more than leave holes in the mare's white cape. The best shot so far just grazed Silvermane's leg.

Silvermane kept dodging the deadly lasers. Her eyes widened a little when the spell finished charging. With one final flash of her horn, the magic vanished from the pointy bone and reappeared as a thick pink disk on Samus's chest.

"This is Boomer's bomb!" Samus exclaimed when she saw the pink disk.

"Oh! You know Boomy? Then you'll probably know just how potent that little bomb is."

Before Samus could respond, the bomb detonated in a massive pink explosion that could be seen from Ponyville. Silvermane had overcharged her bomb, but found herself uninjured since it was still a controlled blast. The explosion had left a big crater, and in the middle of said crater laid the battered form of a Power Suit. Silvermane took a look at it before letting herself collapse, panting heavily; a few coughs escaped her throat. Needless to say, she was exhausted.

It was much to the masked mare's distress that the Hunter rose and looked at her. Even behind the green glass, she could feel the anger in Samus's eyes. The armored human looked like it was struggling to keep afoot, but her arm was steady. The Hunter aimed her cannon at Silvermane. The mare was too exhausted to even speak, so she just closed her eyes and awaited her end.

"NOW!" a voice shouted, and not a moment later, two spiraling rainbows were being directed at Samus. Silvermane opened her eyes to see six mares, one of them Twilight Sparkle, as the origin of the rainbow energy.

Twilight ran as fast as she could, which proved just barely enough to keep up with the ponies that called themselves Land Scout and Misty Breeze. Land Scout she already knew, but Misty Breeze had turned to be a pleasant new encounter. Behind her, Zecora kept up; and Spike was riding on her back. She also noticed a hawk was flying overhead.

As she ran, Twilight couldn't help but wonder if Silvermane would be all right. She had heard news about the mysterious masked hero and her prowess in combat magic, but she also witnessed the firepower Samus possessed. Taking down a creature from Tartarus was a testament to that firepower.

No one spoke until they eventually reached the cage holding the Elements of Harmony.

"We're here, Miss Sparkle." Land Scout announced.

"Twilight!" all the mares inside exclaimed in pleasant surprise. All except Rainbow Dash, who was still knocked out. Zecora and Spike joined Twilight, followed by Land Scout and Misty Breeze.

"Misty! You came back!" Applejack said in delight.

"Of course! It's my duty." replied the light blue pegasus.

"Girls! Are you all okay?" Twilight asked worriedly. She noticed the cracks on Rarity's horn. "Rarity! What happened to your horn?!"

"Samus was very thorough with her hunt. She cracked my horn to prevent me from using magic." Rarity answered. "But don't worry about me, darling. I'll be fine in a week or so."

"We're all a little battered, but fine. Don't you worry none, sugarcube."

"Ok. Brace yourselves; I've had it subtlety." Twilight said as her horn glowed purple.

"What are you doing?" asked Pinkie Pie.

"Getting you out of there."

The cage floated on the air for a bit. Twilight struggled a little as the bars began to bend. A little grunt from the unicorn and the cage was torn to pieces. All the trapped mares fell to the ground. The fall was enough to wake up Rainbow Dash. At their freedom, all the friends had a big group hug; some even shed tears of joy.

"So what now?" asked Rainbow Dash. "Do we go kick Samus's flank?"

Twilight's face had a troubled expression. "That we do." All her friends nodded.

"Then follow me." ordered Land Scout.

All ponies, zebra, and dragon followed the dust-colored stallion. It was time to use the Elements once more.

Princess Luna was concentrating her magic. She had witnessed Samus's ship fly around Ponyville, but it suddenly vanished. She was flying around trying to find it. If the ship could be neutralized, dealing with Samus would become much easier.

She was flying when she felt a disturbance. She couldn't exactly tell what it was, but it felt unnatural. However, the feeling left almost as soon as it arrived. She shook her head and continued with her task.

Luck smiled upon her, for a little after the feeling went away, she heard a low whirling noise. She turned and saw nothing, but a magic field began to form around her horn. The magic field quickly expanded, visible only to her eyes. Within the field, she could see the outline of an invisible gunship poised over the center of Ponyville.

She smiled and dissipated the field. She took hold of the ship in her magic, but cannon protruded from the side of the ship and began shooting at her. Luna barely managed to avoid getting blasted and made some distance from herself and the ship. The cannons kept on trying to shoot the princess down. Luna got as much distance from the ship as she could without letting it go from her sight.

The dark alicorn changed tactics a little. She surrounded the ship in a magic bubble. The cannons reactivated and attempted to blast her, but the shield absorbed every shot. With the ship safely inside her protecting bubble, Luna took hold o the ship in her magic once again. It was hard work, but little by little Luna was able to lower the ship to the ground.

She was halfway down when a loud explosion caught her attention in the distance. It was almost enough to let her lose her concentration and let go of the ship, but she managed to do it. The explosion was very powerful. She could almost feel the shockwave it must've created. Luna thought it was a miracle the forest around was still standing. She wanted to go and find out what that was, but she still had a job to do. She redoubled her efforts and eventually brought the ship to ground level.

As soon as the ship touched the ground, dark chains shot from the ground and tied the ship. Luna summoned more and more chains until she felt sure the ship would be unable to rise. Just as additional security measure, the moon princess erected another barrier around the Hunter's transport.

As soon as she finished, Princess Luna shot to the air and to the place she saw the explosion. "Please be safe, my little ponies."

It was only thanks to years of experience that Samus acted just in time to avoid getting blasted by the Elements of Harmony. "Again!" she heard Twilight yell. Samus watched as the rainbow energy rose again and prepared to jump. What the Hunter didn't expect was to get her body locked in place. She noticed her armor was glowing pink. A side-glance at Silvermane confirmed the hero was still not fully out of the battle.

Unable to move, Samus could do nothing more than see the rainbow energy wash over her. A translucent image of Screwball emerged from her chest. Samus saw as the pink mare twisted and morphed until her body resembled that of a draconequus. Samus watched the image of Discord scream in agony as it slowly vanished, leaving no trace behind. She also barely registered the six mares gasp at the revelation.

The power of Harmony continued to wash over Samus. She felt as if someone torn a piece of her brain and twisted it. She felt all her ideas shuffle and reorganize themselves. The whole process was incredibly painful to her body and strenuous on her mind. Samus let out intense scream of pain as the energy continued manipulating her psyche. Finally, it was over. The last thing Samus took notice of was a message in her visor.

"Harmony energy assimilated. Harmony Beam acquired."

Then, the mental exertion took its toll on Samus and everything went black.