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You wake up in complete darkness, your memories vague and fragmented. The last thing you remember is slipping out of consciousness on your Gunship, its alarms blaring warnings of a collision course with an asteroid belt.
And yet... you feel fine. Cramped a little bit, maybe, but nothing is injured, and when you query your Power Suit for a status report, it reports all systems nominal.
You seem to be locked in some sort of holding facility, and with all communication absent and no idea of where you are or why, it doesn't take you long to resort to more violent solutions. A single Power Bomb takes care of the blocked-off hatch, giving you an exit and destroying the contents of the room in the process.
It doesn't take you long to realize where you are as you stride through the corridors of what appears to be a research station, the B.S.L. logo on the walls of the station a dead giveaway of your location. The station personnel reacts with hostility to your escape attempt, as the alarms come to life, blaring about a research subject breaching the Quarantine Bay.
Not taking any chances, you decide to hide in one of the numerous vents, waiting for things to calm down so that you can explore the station at your own pace and figure out the reasons for your confinement. You aren't sure how much time passes, but eventually the alarms quiet down, and the sounds of movement stop.
You carefully probe with your Power Suit's sensors, and when you find no one in the vicinity, you head for the Operations Deck, eager to find out what's going on. The monitors spring to life under the combined efforts of your deft fingers and the hacking suite of your Power Suit, and that's when your heart skips a beat.
The doppleganger you witness on one of the camera feeds is so similar to you, yet so different, bringing unpleasant memories of Dark Samus to the forefront of your mind. The hideous mockery of your own Power Suit it wears seems almost biological in nature, veins pulsing with a mix of cyan and yellow colors.
You know that if the doppleganger has even a fraction of the abilities you possess, it will wreak havoc if let loose upon the galaxy. You cannot let it leave the station. Hesitantly, you get to work, sabotaging the research station's systems and blocking off entire sectors to cut off the doppleganger's potential escape routes. You hunt it with zealous fervor across the entire station, but the creature (if it could be called one) proves to be slippery, evading you every time you happen upon it, but you know it won't be able to avoid confrontation for long.
Meanwhile, it seems that the creature's presence brought about some sort of corruption upon the station. You aren't sure what the amorphous parasites are, but you also hunt them to prevent their spread. When you first accidentally absorb one of them and feel rejuvenated of all things, you don't know how to feel about, whether it's a good sign or a bad one. Unfortunately, you never have a lot of time to ponder about this as you finally come face-to-face with the doppleganger, cornering it into a fight on the Operation Deck.
The funny, strange and, most of all, horrifying thing about it is that for all the hours you've spent hunting, it only seems to have grown stronger for it, copying your abilities and even mutating them into something different. You are quite sure that Ice Missiles aren't a part of your usual arsenal, and yet, there it is, using them against you.
You struggle with all your might, weaving back and forth, sending blasts of your beams and missiles against the doppleganger, but you are unable to keep up with it. Just when the thought passes your mind that this might be your last stand, the unmarked grave of one Samus Aran, you transform, turning into a hideous, misshapen monster. Unable to deal both with your opponent and the situation at hand, you use your last effort to escape into a different room, as far from the so-called "doppleganger" as possible. After enough time spent regenerating your wounds (because, apparently, as a blob-like monstrosity, that's something you can do), you transform back, turning into the familiar form of Samus Aran.
The pieces of the puzzle fall into place. Somehow, something happened, something that threatened the Samus Aran's life, something that turned her into what you witnessed her to be. You aren't the original. You are just one of the numerous parasites that infested the station. It's unlikely you will be able to communicate with the original Samus of your intent, but you'll have to try.
Will she even be inclined to listen to you, after you've spent numerous hours hunting her around the station, hindering her progress and endangering her life? After you did everything you could to stop her at every step of her way?
With heavy heart and an identity crisis to deal with, you return to the Operations Deck. A brief check of the station's systems shows you the decaying orbit of the station, on a crash course with the planet it's orbiting, the SR-388.
You find it ironic. You can't really fault Samus (if she's Samus, then who are you?) for her straightforward approach to the problem. This is exactly what you would've done if you were in the doppleganger's - in the original's - shoes if you were sent to exterminate a parasitic infestation.
And yet, when you glance through the camera feeds, you see her locked in a struggle with what seems to be an Omega Metroid of all things, and the worst thing about it? She seems to be losing. The realization is all it takes to force you to rush towards the docking bay.
You are still weakened after your previous run-in with Samus, but it doesn't matter. None of it matters, really. If it comes to it, you will gladly sacrifice yourself to guarantee her survival.
After all, if your positions were reversed, you're sure she would've done the same for you.