Note: I don’t know a ton about Metroid and most of what I do know is just stuff I looked up. So, if you really care for the series’ canon, don’t consider this a part of it. It might break with the canon, from what I know of it. But I am doing everything in my power to keep with the total brickhouse badass that Samus should be as a character. I hope that comes across here.
The mighty bounty hunter heaved her quarry into the hold of her ship with a heavy grunt. The door to the cargo bay eased shut behind her and Samus shook her hair loose from her helmet. Her squirming and writhing package was her exact double and Samus had encountered no end of difficulty in capturing her.
It seemed that someone had got hold of her DNA and created an endless army of clones to try and capture her and take her place. For what purpose, Samus didn’t know, but she didn’t really care for the ‘why’ of it. All she cared about was finding out how to stop these damn clones and she had finally captured one of the stubborn things to study its physiology.
The clone was clad in a light blue Zero Suit, much like Samus’ own, and fought hard against the holo-restraints that Samus had placed her within. She had been bound in the bright yellow restraints around the ankles and knees. Her arms were cuffed behind her back and two more of the holo-restraints wrapped around her arms. While taking her back, the clone irritated Samus enough for her to place a heavy muzzle over her mouth to keep the clone silent.
Samus closed her eyes and let out a heavy breath. In moments, her Power Suit dematerialized and Samus herself was left in her own blue Zero Suit, identical to the one worn by the clone. But Samus had noted that none of her clones seemed able to summon a Power Suit of their own. This gave her an advantage in combat against them and she was able to best them, even in groups.
They always fled before she had a chance to capture or destroy them but the slippery things had finally gotten complacent enough for her to catch one.
The clone glared up at her captor and struggled against her restraints. She growled at Samus behind the big muzzle that gagged her but she made hardly a sound. Samus plucked the paralyzer from her hip and pointed it in the clone’s face.
“Quiet,” she said, without a hint of emotion in her voice.
The clone ceased her struggling and simply glared at the bounty hunter. When the clone stopped moving, Samus replaced the paralyzer at her hip and removed a scanner from the wall. Samus pointed the scanner at her clone and it scanned her entire body in a brief flash. It took her a few seconds to digest the information on the readout screen.
It seemed the clone was just as human as her, though she perhaps lacked some of Samus’ cybernetic enhancements. She supposed it was difficult to replicate a human perfectly and even harder to replicate her. The most successful replication she had ever seen was... well, she didn’t like to think about that.
More information flashed on the scanner’s screen. Trace elements of phazon fused within organism’s biological structure. Phazon? Samus had wiped out that stuff’s origin herself. But her scanner never lied, she knew this herself, so then it must have been possible that someone had found another source of the poison. Maybe another planet like Phaaze had been created by a Leviathan outside the galaxy? If that were true then that would be yet another problem to deal with. But she would find that out in time.
One further bit of information on the scanner almost made her drop it. DNA evidence of the Metroid being known as Prime. Metroid... Prime? That didn’t seem possible. Samus had destroyed that damn creature. There was no way it could still be alive. And it had her DNA to create clones? That was when it hit her.
“Damn it,” she cursed to herself. “It’s her.”
Dark Samus. That would explain everything. They shared DNA, after all, when that cursed Phazon Suit merged with the Metroid Prime. That had to be why the clone had trace elements of Phazon and both her and Metroid Prime’s DNA. Samus could only guess how it was that she had come back after she destroyed Aurora Unit 313 back on Phaaze. There didn’t seem to be any way for her to have come back and it was entirely possible that Samus was making an incorrect logical leap.
For now, though, Samus would get this clone back to HQ and figure out more about its origins. She hoped her suspicions weren’t correct.
Even the Space Pirates feared Dark Samus when she was around. Her cold cruelty made her perhaps even more feared than Samus herself. Dark Samus would always kill with impunity which was the one thing Samus couldn’t explain. Her own dark reflection never bothered to try capturing her opponents before. Anyone in Dark Samus’ way would always have been killed in the past, even allies. It was quite unthinkable that Dark Samus would try anything but to kill Samus. What was she hoping to accomplish by replacing the bounty hunter with a clone?
Samus replaced the scanner on the wall and shut her captive clone away within the sectioned off room of her cargo bay. As she began the climb up to the cockpit, several pairs of eyes watched silently from the cargo bay, waiting.
...
Samus stared out at the endless grey plain before her for a few moments. The planet she had landed on was nothing but a barren wasteland that had gone unnamed for some time. Some explorers had been here, however, and set up an outpost a few hundred metres from her landing site. They had sent up a distress signal that they were under attack by... Samus Aran. It seemed that the news about the clones hadn’t entirely gotten out yet. The explorers were quite relieved when the real Samus Aran had arrived to fight off the horde of clones. How many had been created?
Each time, Samus had to fight off eight to ten clones and sometimes more. Were they always the same ones who fled or were they all over, wreaking havoc? Whatever the answer, it didn’t matter. Just striding in with her Power Suit was enough to scare them off. A few would try to stay and fight but they quickly found out that was a bad idea.
Samus had wounded a few of them in battle but the clones were always quick enough to escape. One of them had let slip the plan by accident once when they thought Samus wasn’t paying attention. She had allowed them to creep up behind her and whisper the plan back and forth and when they were within striking distance, Samus whirled on them and knocked one flying with a vicious and heavy kick to the chest. The other tried to flee but Samus decided enough was enough then. The last clone in that explorer’s outpost soon knew the fear that came with being a target of the Bounty Hunter Samus Aran.
Relentless in her pursuit, nigh invulnerable behind that armoured suit and even without it, with strength like a bear and unparalleled determination, the clone learned that there was nothing to stop Samus when she set her sights on you.
Now Samus had captured the clone and kept her in the cargo bay. The clone had tried to act defiant but anger is often a way to cope with fear. And every target of Samus Aran knew the tremendous depths of fear.
With the stubborn clone finally dealt with, Samus had chosen this time to relax a bit while she did the pre-flight checks in the cockpit. She had changed out of her Zero Suit and into her casual clothing, which was an orange cropped, sleeveless shirt that clung tight to her body and left her midriff open to the air and a pair of matching, tight short shorts.
The outfit revealed her thick, toned leg muscles and rippled stomach. People always thought she would be thin and lean under her suit. Samus was rather lean, sure, but even out of the suit Samus was strong and intimidating. Her cold-eyed stare and muscular arms would make anyone think twice about starting a fight with her. Unless they had a death wish, of course.
With her checks completed and everything green to go, Samus reached to fire up the engines when she felt the hair on her neck stand on end. Someone was watching her. Her paralyzer gun was across the room, too. When she froze, she heard someone dash away from the cockpit and she leapt over the seat and charged after them. Grabbing the paralyzer from the wall, Samus rounded the corner and was forced to duck away when a fist came flying toward her head.
“Pin her down!” came the sound of her own voice.
Another fist whizzed past her head from a different direction and Samus took in her situation. The other seven clones on that outpost who had fled now surrounded her on all sides, each identical to her in almost every way. But they were all in Zero Suits while Samus was in her casual outfit. It might be harder to get into her Power Suit like this so Samus opted not to for the time being.
One carefully aimed shot of her paralyzer knocked one of the clones down but three others rushed at her. Samus dug her heels in and pushed upward with her powerful legs to launch herself into a high back flip. She leapt over the heads of the three clones and planted two of them with thundering kicks that sent them backward into the corridor walls.
The third threw a tentative punch at Samus' head but the bounty hunter swiped her hand aside with ease and countered with another point blank shot of her paralyzer. The remaining four came at her all at once. One of them managed to land a glancing kick off her shoulder but Samus was quick enough to avoid the rain of blows. However, two of them managed to get hold of her arms while she moved and tried pinning them behind her. Samus almost chuckled at their weak effort.
With an incredible surge of strength, Samus pulled her arms apart and lifted both of her clones of the ground. She gripped both of their heads and slammed them together, knocking both clones unconscious, and they crumpled into a heap at her feet.
The two clones she kicked earlier returned and now the four still left standing closed in on either side of Samus. Despite being like her in almost every way, Samus could see the fear in their eyes as they crept closer to her. They weren’t as fearless as she herself, it seemed.
Once again, four clones leapt upon her and succeeded this time in pinning her down. One of them reached to her belt and removed a pair of high security handcuffs to restrain Samus with. But her eyes opened wide when a mighty arm worked itself free and a jolt from Samus’ paralyzer froze the clone’s body. The clone collapsed to the floor and the handcuffs skittered away, useless.
With another surge of strength, Samus pushed herself back to her feet and made the three clones stumble and fall. Using the last charges of her paralyzer, Samus spun and fired a shot at each of the clones to keep them down and subdued on the ground.
She took a moment to catch her breath and look around at the floor around her. Seven on one, and in tight quarters, and these clones had failed to take her down again. It was starting to seem too easy now.
Just as the thought hit her, a dark figure appeared out of the corner of her vision. Before she could react, the lightning speed of the figure zapped her with some kind of stun bolt and Samus fell to the floor with the clones she had just defeated.
A woman let out a low chuckle and stepped closer to her. The dark, armoured figure stood over her and Samus saw then what she had feared. Dark Samus' black visor stared down at her and Samus could see down the barrel of her arm cannon as it was pointed in her face.
The dark armour dissipated and revealed another identical face to her own and a woman in a black and red Zero Suit. The woman’s hair was tied back in a ponytail like Samus but it was jet black instead of Samus’ blonde. Samus’ own blue-green eyes were replaced with a vicious red and Dark Samus smirked at her stunned opponent.
“Misdirection, Sammy,” Dark Samus said. “I knew you could never resist a fight.”
How long had Dark Samus been on board her ship? She must have cloaked herself somehow, just like before.
“No more direct fights, Samus. We both know how that turned out last time. And I can see you haven’t changed a bit. Let’s get you put away.”
...
Samus could feel her ship lifting off the ground but there was nothing she could do. The clone she had captured still scowled at her and struggled with her restraints. But Samus noticed muffled laughter coming from the clone when Samus herself was dumped into the cargo bay by her dark reflection. She still didn’t know what Dark Samus’ plan entailed, exactly, but that didn’t matter to her right now. Escape was the only thing on her mind and she knew her clone captive would be no help to her.
Samus had been restrained much like the clone herself, except her holo-restraints glowed red. That meant they were a security level higher than the clone’s restraints. They kept her legs bound at the ankles and above and below the knees. Three of them hugged tight to her strong arms and a heavy pair of high security handcuffs kept her hands trapped behind her back. Topping it off was a red, glowing panel gag that muffled any of her protests and kept her as silent as the restrained and gagged clone beside her.
She tested the restraints and struggled a little bit but they held on very tightly. No easy escape this time, it seemed. But Dark Samus hadn’t taken into account that Samus had the release for these restraints. After all, her dark reflection had only raided Samus’ supply of prisoner transport restraints. Samus knew exactly how these worked. It would be difficult, of course, and it would take a little bit of time but she knew this planet was well beyond the Federation border. It would take time for Dark Samus to reach HQ and it would be plenty of time for Samus to retrieve the release. Now it was just a matter of finding it.
With her ship taking off into space, Samus pulled hard against her tough restraints and pulled herself up into a sitting position.
“Mmph!” she grunted.
“Hmmph?” the restrained clone said, growing worried at the sight of the resourceful bounty hunter moving without fear, even while restrained.
Being the incredible athlete that she was, Samus managed to hop to her feet. Her heeled boots clanged on the metallic floor as she stood up straight. With a few deft hops, Samus reached the wall and struggled to get her hands up to the door release on the wall. She reached the button easily and it slid open before her. Across the cargo hold, hanging near the bay door, hung the release for her restraints. Samus smiled beneath her gag when she realized that freedom was only a few short hops away. The clone furrowed her brow, her worry increasing, as Samus took a confident hop forward. Her escape was no longer an if and was now a matter of when. Dark Samus wouldn’t know what hit her.