A problem that arises when you have continuous sequels (sequels that take place after the events of another game) is power. Basically, how do you explain power loss. The 2D Metroid games have been poor with this, with one notable exception, being Fusion. The basics is that Samus gets infected by a X Parasite which basically replaces a host piece by piece until they are effectively the same person, but heartless. The Federation had to use a Metroid vaccine, since Metroids are the X's predators, to save Samus. But they had to surgically remove parts of her suit since they effectively combined with Samus. The pieces removed were stored (but not decontaminating it for some reason), but reformed thanks to the X in it to form SA-X.
In the game, most of the upgrades were Core Xs (basically a group of Xs together) that gave the upgrades. To compare, here are the powerups from bosses
Morph Ball, Charge Beam, Hi Jump/Jumpball, Speed Booster, Varia Suit, Wide Beam, Space Jump, Plasma Beam, Gravity Suit, Wave Beam, Screw Attack, Ice Beam (kinda)
And here are the powerups given via
Missiles, Bomb, Super Missiles, Ice Missile, Power Bomb, Diffusion Missile
I think part of the intro will show Samus losing the X she absorbed through fusion, which also results in her losing her ammo and health since they were also responsible for giving that. In other words, she loses her powerups from X, which also leads to her losing her Missiles and Super Bomb upgrades, leading her to only know Bomb, but no Morph Ball. But I think her being part Metroid does lead to her suit being different. She's evolving similar to a Metroid. Since it's implied that the Metroid Queen at the end of Fusion (oh yeah spoilers) escaped the Restricted Area and absorbed enough X to become a Queen over the course of a hour or two. I think Samus absorbed enough X for herself to evolve slightly, leading to a suit more reminiscent of the Varia suit, but I think that a certain X is going to be the secret final boss. I think at least one SA-X escaped the BSL station since...
We know there is at least 10 in Fusion and only 1 was killed by Samus herself. As it's a space station with hostile creatures, it probably has escape pods. If they were as smart as Samus, at least one would flee as soon as the timer starts ticking, as time limit escape sequences are Metroid staples. So... what's important about the number 7, maybe it's because 7 SA-Xs are still out there. On that planet. Which is why BOTH the EMMI and Samus are there. The EMMI was stated to be there because of X being there, but we don't know why Samus is there, especially after a rocky time like Fusion. I think she knows this is where the remaining SA-Xs are, so she wants to personally hunt them as they are her responsibility.
This would also explain why Samus is hunted on sight by the EMMI. They are hunting the SA-Xs. They lack biological parts to avoid the control and are specifically made of Samus-proof materials. Although I 100% expect the Omega Cannon to become a permanent upgrade at the end thanks to the original Mother Brain or one of her infinite redos. Specifically to fight off the EMMI, which are all hunting HER as, by this point, the SA-Xs that roam the areas are all dead and she absorbed their X Cores. Maybe this could even give her some of her older abilities, like the oddly missing from Treehouse Morph Ball. So she has all of their signatures and the EMMI of each area know it and target her, leading to a big finale of Omega Cannon Samus vs 7 EMMI.
TL:DR. Samus could lose her powers thanks to the X getting drained from her and the SA-X might still be alive.
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