Note: This is a sequel to my story Metroid: Hunting the Clones but it can be read on its own. I’ll link to the first story in case you wish to read it as well. Enjoy!

The door hissed shut behind her as Samus continued hopping across the cargo bay. After her latest surprise encounter with Dark Samus, the bounty hunter had been quite thoroughly restrained and gagged in her own high security restraints.

Escaping the small room of her ship’s cargo bay hadn’t exactly been difficult, however, as every switch and sensor was coded to respond to her. And Dark Samus hadn’t bothered to check for the release to Samus’ red restraints.

The mighty bounty hunter was still dressed in her casual workout clothing; an orange, cropped and sleeveless shirt that bore her strong abs and a matching pair of tight short shorts. Her black, heeled shock absorption boots clacked on the metal floor with each subsequent hop toward the release for her restraints.

The glowing red, high security holo-restraints kept Samus bound at the ankles and above and below the knees. Three more hugged tight to her arms from her forearms to just below her shoulders. The high security handcuffs on her wrists were heavy and weighed her arms down slightly as they were kept restrained behind her back. She grunted into a red, glowing panel gag with each hop toward freedom.

The red, glowing release for her restraints would drop everything off her body at the press of a button and only responded to her command. Dark Samus didn’t take that into account, of course, and now Samus was only a few steps from freedom.

She wobbled a bit on her feet when the release that hung by the bay door was finally within reach. The heavy restraints made balance difficult even for a strong, athletic woman like her but she managed to retain her balance and stay standing upright.

Grabbing the release was a struggle and Samus grunted in frustration every time she failed to grab the release but, with a deft hop in the air and some awkward twisting, Samus got the thing off the wall and into her hand.

Samus sighed with relief when she finally had a hold of the thing and pressed the button. In an instant, the locked latches on every restraint popped open and Samus was free once more and with her enemy unaware.

Each of the restraints dropped to the floor and the red glow dissipated into a dull grey. Samus stretched her muscles and worked her jaw for a moment. Her steely, green eyes rested on the ladder up and out of the cargo bay and on toward the cockpit. Dark Samus and seven of the clones of Samus she had created were up there, steering her ship to somewhere. Samus didn’t know or care where they were going. They wouldn’t get there.

Picking up the holo-restraints, Samus eyed the storage room where she kept her Zero Suits and rows upon rows of power armour. She realized that her supply of prisoner transport restraints was not enough to restrain all seven clones and Dark Samus herself. She only had enough for two more prisoners. Thinking on her supply of weapons, she remembered her autotaper. It wasn’t ideal and was usually used to seal packages of cargo shut but Samus knew the glowing, purple tape was strong enough that even she might have trouble breaking it. The clones, then, wouldn’t stand a chance of getting out of it.

Walking to her Zero Suits, Samus once again donned her light blue outfit and tapped a standing tube with her familiar power armour inside. With a single thought, Samus was fully armoured, armed, and ready for battle. It was time to work.

...

The clones patrolling the upper floor of the ship were surprisingly dull-witted. Despite being clones of Samus herself, none of them possessed her acute senses and quick instincts. She made short work of the first three, taking them out one at a time. Samus fired her autotaper and wrapped each clone from the shoulders to the waist in the purple tape. A quick shot at their heads wrapped the tape around their mouths and she dragged each, one by one, down to the cargo bay and finished by taping up their legs.

Each clone was then stuffed into the separate room where a restrained and struggling clone already was, bound tightly in yellow, medium security holo-restraints. Samus had caught that clone on the planet she had landed on and heading to that barren place is what started this whole mess in the first place.

Four writhing, squirming captives lay in the separated room now, unable to escape, grunting and growling their muffled protests into their gags. Samus smirked slightly at the sight. Only a few minutes ago, she was in that room, struggling away in her own restraints. How quickly things could turn around.

There were still four clones remaining, however, and Samus could feel her ship starting to move faster. Wherever they were heading, she wouldn’t have much time to reverse course and get the drop on Dark Samus.

When she returned to the upper floor, still dressed in her Power Suit, Samus decided on a more direct approach. She waited for two of the clones to spot her and let them charge straight for her. Samus noticed the fear in their eyes when they saw her in the power armour but something compelled them to fight her nonetheless.

Samus flicked her arm cannon and a stun whip emerged from it, sparking and crackling in the air. The first clone to reach her got a taste of the electrical energy and was brought down to the floor, knocked unconscious by the quick movements of the mighty bounty hunter.

The second clone was taken down quickly as well, trying to dodge one way and attack Samus’ flank but, with her lightning reflexes, the bounty hunter simply stepped to one side and lashed out with the whip once, connecting with the clone’s chest and sending her sprawling to the floor, unconscious beside her clone ally.

Samus had them taped up, gagged, and stowed away in the sectioned off cargo bay room in minutes. Now with just two left, Samus was almost done in reclaiming her ship. She knew the clones would be easy work but Dark Samus might have another trick up her sleeve.

Dark Samus had cloaked and hidden aboard Samus’ ship and managed to get the drop on Samus and restrain her. But now the odds were in Samus’ favour, though she refused to underestimate her dark counterpart.

With the autotaper holstered at her side and her arm cannon at the ready, Samus climbed back up to deal with the last two clones. Once again taking a direct approach, Samus tuned her arm cannon to a heavy stun projectile, taking aim at the two clones who came patrolling out of Samus’ engine room. The first didn’t even know what hit her when a sparking, blue beam of light connected with her forehead and took her to the floor, knocking her out. The second tried to rush Samus but the bounty hunter took careful aim and fired off another stun shot to incapacitate the final clone.

With a second set of medium security restraints in hand and the autotaper, Samus set to work taping up one clone and gagging her. She bound the other in her prisoner transport restraints and gagged her with more of the tape. Taking them both down to the cargo hold, Samus locked the door to the room now with eight mewling captives and slammed it shut. Now it was just her and Dark Samus.

Up in the cockpit, Dark Samus was still piloting and navigating the ship. Samus didn’t make a sound as she approached her own dark reflection. When she had first been captured, Samus was surprised to learn that Dark Samus now had a more human form and even her own black and red Zero Suit. Dark Samus’ hair was jet black and still tied back in a ponytail, identical to Samus’ own hairstyle. Samus remembered her dark twin’s vicious red eyes and much paler complexion and still felt startled by the image. To see her own face stare back at her with such a vile look in the eye was just unsettling.

But Samus remained focussed and raised her arm cannon to charge it, knowing Dark Samus would hear.

Dark Samus stood from the pilot’s seat and turned around quickly, pointing a dark version of Samus’ paralyzer back at her. The two of them stared each other down for a few moments when a wry smirk curled Dark Samus’ lips.

“You’re quite the escape artist, Sammy. How’d you pull that off?”

Samus said nothing and stepped closer, the cannon still charging up and beginning to glow blue from the energy pulsating inside.

“So what are you going to do? Kill me again? Give it a try. But at least let me even the odds.”

Dark Samus all black power armour appeared on her body in seconds and that was when Samus let loose her charged shot. The blue ball of energy connected with Dark Samus’ armoured chest and sent her stumbling backward.

Samus leapt at her opportunity and rushed her dark counterpart, laying a heavy shoulder into the woman. Dark Samus was knocked clean off her feet and landed on the floor on her back.

Dark Samus was quick to get back up, however, and deliver an uppercut to the underside of Samus’ helmet, causing her to stumble back a bit. Charging her own arm cannon, Dark Samus let fly a dark red projectile straight on toward Samus head but Samus was able to think quickly and deploy a light shield to absorb the attack.

In one motion, Samus recovered and rolled forward, sweeping out Dark Samus’ legs with a quick kick of her own before leaping on top of her and blasting her helmet full on with a charged stun shot. The powerful blast was enough to make Dark Samus power down and eventually fall unconscious with the bounty hunter still on top of her.

Reaching back for the high security restraints and panel gag, Samus smiled and allowed herself to revel in her victory for just a moment before she started binding Dark Samus. With her fully bound in the restraints that once again glowed red, Samus hauled her quarry back down to the cargo bay with her eight clone captives.

A cacophony of gagged grunts and growls greeted Samus’ ears as she opened the door and tossed Dark Samus to the floor. She propped Dark Samus up against the wall and allowed her power armour to dissipate. Samus stared at Dark Samus’ face, waiting for her to wake up again.

Dark Samus finally came around and found herself staring into the piercing green eyes of the mighty bounty hunter before her.

“Sammy...” she said, a faint taunt still in her voice. “You’re still here?”

Samus said nothing and leaned in close to Dark Samus once again.

“How are you alive?” she asked, gritting her teeth.

“Wouldn’t you like to... hey. Why can’t I move my arms?” Dark Samus shuffled in her bonds and realized then that she had been very effectively restrained exactly how Samus had been. The sound of her clones’ muffled cries entered her ears then and she saw the writhing pile of women, all identical to Samus, all bound and gagged and struggling away on the floor.

“No!” Dark Samus said, thrashing in her bonds. “You can’t do this! I... I’m not the real Dark Samus!”

Samus smirked. “Who are you, then?”

“I... I’m a clone.”

“Who made you?”

“I don’t know! But I was just a bounty hunter like you! I swear it! I was captured by this target I was after and they... changed me. I don’t know where they got the Phaaze, or your DNA. Honest.”

“Why not say this before? How do you even know who I am?”

“They programmed it into me! I don’t know how any of this stuff works! My brain has been fighting it this whole time, though, trying to get me back. It only worked when you beat me and put these... things on me. Do they have to be so tight?” ‘Dark Samus’ asked, fighting her bonds again.

Samus just nodded and digested Dark Samus’ words. The two women remained silent while ‘Dark Samus’ continued to struggle. “So... so will you let me go? I told you the truth, I swear it! Please?”

“Where were you going to take me?” Samus asked.

“The person’s base, I think. I don’t know! I can’t remember anymore! Please, just untie me!”

Samus nodded again.

“Samus! I’m sorry! Please, let me go! I won’t come after you again, I promise! Untie me, please!”

“You say you’re telling the truth?” Samus asked.

“Yes,” ‘Dark Samus’ said, nodding.

“We’ll find out.”

“What? What do you mean? Wait, what are you doing!? No! No, pl-mmmph!” Samus pulled the panel gag tight over the mouth of ‘Dark Samus’ and allowed the latch to snap shut behind her head. It glowed red like the rest of her restraints and silenced her completely.

“Mmmph! Nmmm! Plmmph dmmt dmm thmmph!” ‘Dark Samus’ pleaded.

Samus said nothing more and stood up again. She flicked the door switch and allowed it to open. As she walked out, ready to lock the door behind her, Samus brandished the red restraint release at ‘Dark Samus’, showing her how she had escaped. Attaching it to her belt, ‘Dark Samus’ squealed in fright and struggled in her bonds but she just couldn’t escape the high security holo-restraints and heavy duty handcuffs locked around her wrists. And with Samus carrying the only release to her restraints, she was not going anywhere.

Samus allowed the door to hiss shut behind her once more. Climbing back up to the cockpit, Samus managed to slow her ship’s path and change the navigation to the nearest Federation prison. It was there that she would find out the truth for certain.

Thinking back on her interrogation, Samus realized the genuine fear in the eyes of ‘Dark Samus’ meant there might have been a bit of truth to what she said. It had been much easier to defeat her this time, after all. It would explain a lot. But that would have to wait for another day. For now, Samus had escaped her clones and some strange copy of ‘Dark Samus’ and regained control of her ship. All in all, a good day.