This is not a pairing, this is for fun.
Dark Samus is an "it" to avoid confusion...

Samus sat in her room, glaring at the ceiling for an unspecified reason.
Suddenly there was a knock at the door, causing Samus to jump in surprise.
She grabbed her gun and slid against the wall, edging carefully over to the door panel and opening it.
When nothing ran inside to attack her, she slid her head round the door, checking the corridor in puzzlement.
It was only when she closed the door did something happen, a blast of Phazon Energy paralysed her body but left her mouth and eyes to work continuously.
Slowly she managed to regain control of her vocal cords...
"Who's there?" growled Samus before adding "...and if it's you Ridley I'm going to string you up by your guts and..."
She was silenced by a sharp kick to the gut, before having her head turned upwards to see her captor...
"You..." she whispered as she felt her numb body tense in preparation...
"Me..." said Dark Samus, the acid green visor seemingly grinning at Samus Aran.

Samus was dragged through the ship to the prison unit, where her arms and legs were chained to the ceiling and floor respectively...
"What do you want, Dark?" she asked with a numb tongue, trying and failing to shake the paralysis from her body.
To her surprise Dark Samus' armour began to melt away, revealing what may be described as her shadow.
Its eyes were devoid of pupils, only blood-red irises filled the white space.
Instead of straight, blonde hair tied into a ponytail Dark Samus' was black, loose and wavy.
Its face was more rounded than hers, but the bodies were almost symmetrical...
"What do I want, Samus?" it questioned, circling her "I want all the power in the universe, I want beings to bow before the might of Phazon..."
It then appeared in front of her, pressing closer to Samus' body so she could feel the heat of the being.
Then, with its hand it roughly moved her head to the side, moving closer until its mouth was level with her ear...
"But first..." it whispered seductively into her ear "...First, I want you..."
Samus' eyes were wild with confusion, what was Dark talking about?

Dark drew back and fished into her body, revealing a...
"Ball-gag?" stated Samus, before she was slapped across the face and found it forcefully strapped into her mouth.
Dark then proceeded to run its hands down Samus' body, savouring her curves and rubbing her sensitive areas.
One such area was around her clit, to which she let out a small whine of disapproval...
"Oh, so you do have a weakness, hmm?" it said, raising itself back to its full height and massaging her breasts, playing with them like surreal toys "Well then, lets expose it..."
In an instant Samus found her Zero-Suit being peeled away from her body, exposing her pale skin that she had kept armoured all this time.
Samus felt Dark slide down her body like a snake, tracing her breasts with its wet, slithering tongue.
It went further south, the tongue lapping over her curves until it visited her clit.
Dark parted the pink flesh gently, suddenly ramming the tongue inside and molesting her insides with an orgasmic fury.

"But of course, we can't stop there..." said Dark Samus, suddenly getting up and clamping a circular object to her wrists and ankles.
Samus began to sweat; she instantly recognised the objects as Shock Chains, a type of cuff that the Federation used on dangerous, unruly criminals.
Samus wanted to plead but the ball-gag only allowed her saliva to flow in streams from her mouth, which, to her horror, Dark noticed...
"What's that Samus, something to say?" it said, tilting her head in mock confusion.
It strode towards her, grabbed her hair and forcefully tilted it back to reveal her neck.
Dark began to molest her neck, stroking and biting playfully until it lowered her head and began to ravage her face, using its tongue to spread the streams of saliva over her skin and into her ears.
When Dark had finished, Samus had felt the numbness subside enough to allow her to walk.
Dark turned to her with a malicious glint in its eye...
"If you attempt to flee, you die..." it stated, holding the control threateningly "...and if you don't comply with my needs, you also die..." it continued, unclamping Samus so she dropped to the floor.
It attached a collar to her neck and leashed her to its hand before bending down, grabbing her hair and pulling her upright...
"Lead me to your quarters, slave..." it spat the last word into her ear "...and we can continue there..."

Samus led her enemy to her bedroom, in which the leash was attached to the ceiling and Dark sat on Samus' bed.
The Chains were clamped together to form cuffs on her wrists, making her look harmless and helpless.
Dark looked at her with indecision before coming up with a fitting punishment...
"Lick my feet, or else..." it said, snapping the ball-gag from its place and extending its foot.
Samus reluctantly wiped away the loose saliva; it had got on her nerves as well as her eyelids...
"And what if I don't?" she spat instantly, to which Dark raised the control...
"Go ahead, make my day..." growled Samus, ready to defy her keeper for the last time "...you'll get no prize and I'll be away from you forever..."
Incredibly, Dark tossed down the remote, threw Samus to the floor and converted its hand into a mass of tentacles...
"If you don't comply with my wishes..." it said maliciously, lowering the writhing mass "...then this happens..."
Instantly Samus found one tentacle wrapped round both of her breasts, one attacking her mouth, one ramming itself up her tight ass and two molesting her clit.
Samus began to get hotter; a deep red blush echoed over her face, her sweat had begun to trickle down her in pools and the orgasmic juices that were collected by the tentacles were spread over her body and face.

The whole experience lasted ten minutes, before Dark knelt down and bought Samus' body close to its own...
"I enjoyed that..." it whispered seductively, licking her face with its snake-like tongue "...but disobey your orders again and I will make it ...painful..."
Dark breathed the last word into her ear, before lapping up the last of the juices that were in the area, much to Samus' displeasure.
It then knocked her from her feet, returning to the bed and held out its foot...
"Lick..." it commanded, moving it to Samus' mouth before continuing "...lick, passionately..."
Samus, against all overriding options, did so.
She was therefore surprised when she discovered that Dark Samus did not taste of Phazon, but of liquorice...
"That's right slave, now the other foot..." came the voice of its owner, moving the well licked foot away and replacing it with a clean one.
However, as Samus was about to begin on the other foot Dark suddenly flipped her over, shoved the ball gag back into her mouth and spread her out on the floor.
Samus' eyes widened as Dark's hand once more became a mass of tentacles, this time she would have it blindfolded.

Samus' body twisted and writhed as she felt the tentacles play with her insides and molest her breasts until they were sore, then something wet and sticky rubbed against her stomach.
Dark Samus slid its clit over Samus' stomach, receiving a large amount of drool from her mouth which Dark quickly spread over her face with its tongue.
Samus' back arched in ecstasy, to which Dark then rolled her over and began to kiss her back passionately, massaging its clit down her leg and whispering seductive things into her ear.
Continuing to talk sweet nothings into her ear as it rolled her over, ready to play with her insides again until one such thing made a lake of drool bubble from her mouth.
Dark lapped this up, this time spreading it round her clit and using the tentacles to massage her breasts until it heard Samus wail in pleasure, instinctively placing its tongue over her clit as Samus cummed violently.
Samus was exhausted, but the years she had gone with no sexual interaction were paying off in these moments.
Dark raised itself up, a mouthful of Samus' cum washed over its owner, the latter drooling from her mouth even more.
Dark tore off the gag, threw it away and planted a passionate kiss on her lips, the tongue savouring every last drop of saliva that was contained in her mouth.
Samus felt the tentacles begin again, but before Dark knew what was happening Samus rammed two fingers into its clit, both bodies releasing moans of pleasure as Samus carried on sliding the fingers around its clit while Dark fucked her insides with the juicy tentacles.

This time Samus engaged a kiss, but it was batted away by a tentacle and she was pinned against the wall, her clit and boobs sore from the fucking...
"You dirty bitch..." whispered Dark, throwing her to her bed "...I'll fuck you so hard you'd wish you never attempted that!"
Dark went all out on Samus, the tentacles reaching 12 inches inside her defenceless body, the sheets wet with cum from both bodies and Samus attempts to scream in pleasure while three inch-thick tentacles devoured her mouth.
Samus felt a hot, sticky area press over her face, none other than Dark's clit.
The tentacles jolted backwards and forwards faster than before, her enemy's cum drenching her face and in one orgasmic scream the tentacles had deposited their liquid gold inside Samus.
Unclasping the Chains and tying its victim to her bed, Dark Samus slipped back into the shadows as silently as it came.

Samus awoke with a start, finding herself safely in her zero-suit and her arms free from the bed.
Giving herself a quick shake to wake herself up, she headed towards the shower unit and found a note taped to the mirror, it read...

Don't think I'll pull this off once, however far you think of me as your dark enemy.
Just a warning...

~DS~

Samus screwed up the paper and threw it behind her, she knew she had to go and kick its ass...
But she'd beat up Ridley first, that always put her in a good mood...