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There will be a secret ending that alludes to Metroid Fusion
We see a lone hornoad hopping about in the caves, minding its own business. From a small crack in the ground we see an orange blob ooze out and slowly rise into the air. It suddenly flies at the hornoad, enveloping it and seeping in through its skin. The hornoad convulses...
  • Confirmed, as least as far as the final cutscene alluding to Fusion is concerned. It even involved a lone hornoad hopping about minding its own business.

Just like Zero Mission, the original Metroid II will be available as a reward for completing the game.
Because what better way to celebrate the remake of a lesser-known sequel than to include the original?
  • Jossed.

Ceres Space Station will be available as a Bonus Dungeon if the player reaches 100% completion.
It will feature a heavily revamped boss fight with Ridley as a crazy True Final Boss and act as a Sequel Hook to a Super Metroid remake.
  • Ridley being the final boss is confirmed, everything else is jossed.

Nintendo will include Another Metroid 2 Remake as an unlockable bonus
It's pretty clear from various interviews that there's no animosity between Nintendo and Guasti over the takedown; Sakamoto has admitted to having heard of the game while working on Samus Returns and Guasti has defended Nintendo's actions and praised the official remake. It's also rumored that Nintendo deliberately waited until after AM2R's release to issue the C&D to allow people a chance to download it first. Despite this there are still many who paint Nintendo's action in a malicious light and portray Guasti as a victim. So what better way to quell these arguments than to include the fan remake with the official remake, thus giving it official Approval of God?
  • This does not seem likely due to the fact that AM2R was both released and C&D'd so close to the release of Samus Returns. It would require additional play and bug testing and potentially push back the release date; it's likely the MSR was already in the manufacturing stage by then. AM2R also was not designed for the 3DS, meaning it would likely need to be rebuilt from the ground up to ensure that it's properly compatible.

The Aeion Abilities Samus receives in this game are the Psychic Powers the Chozo demonstrate in Metroid Prime
While Samus clearly won't be gaining the ability to see the future, Aeion grants her limited ESP through the Scan Pulse, which reveals the secrets of her surroundings. Her other Aeion powers seem supernatural in origin, even though most of Samus' arsenal has been gadget-based. It's possible the Chozo isolated the source of their psychic powers and figured out how to imbue others with it.
  • Jossed. They come from the natural planetary energy of SR-388 and its native organisms. The implication that the Aeion is what caused the Metroid to start mutating seems to indicate that the Chozo weren't fully aware of what it was or what it could do.

Ridley is the one in the recent Direct
I Mean come on, the Direct shows that whoever was in it is someone who's out for revenge against Samus and the clips show that it's some kind of monster. It has to be Ridley.
  • Confirmed, in the form of Proteus Ridley, a mostly-regenerated Meta Ridley.

The game will lead into a Video Game Remake of Super Metroid and/or Metroid Fusion

  • In the vein of the original Metroid being remade into Zero Mission and the sequel being remade into Samus Returns, the other two 2D Metroid games will receive updated remakes; especially since MercurySteam wanted to remake Fusion in the first place.
    • With how beloved it is in its current state, I doubt Nintendo would allow for a remake of Super, but with all the allusions to Fusion, this seems to be a strong possibility. This troper doesn't see MercuryStream coding in an entire scene with a retextured Hornoad and a completely-unused-in-game X-Parasite model just for a cutscene alone.
    • The Legend of Zelda: Ocarina of Time showed that Nintendo is perfectly willing to allow remakes of their most beloved Sacred Cow games, provided the developers handling those remakes know what they're doing. Samus Returns may have been Nintendo vetting MercurySteam for the job of remaking Super Metroid by having them remake the less-sacred Metroid II: Return of Samus, first.
    • The Zelda remakes are not nearly as drastic as the Metroid ones. The graphics and some mechanics were tweaked but the structure and design of the original game is sound, unlike Samus Returns and Zero Mission.
      • Although that may not stop a more faithful, Hi-Bit remaster of said games.

The Rogue Warrior Chozo
  • They will be the antagonists of Metroid 5, because no way do you leave a Sequel Hook of that nature around and not build up to it.
    • Alternatively, they could be the antagonists of Metroid Prime 4, where they make their own version of the titular Metroid Prime.
      • Metroid 5 seems more likely, as the series' chronology has the Prime series set before Samus Returns, and when the image first appears, it's listed as 2d/10 instead of 11/11.
    • CONFIRMED! They are indeed the antagonists of Metroid 5, which is none other than the near-mythical Metroid Dread.

The Diggernaut actually didn't go rogue after all
It was enraged by the warlike Chozos' murder of its creators. As Samus Aran just so happened to be wearing Chozo power armor, the Diggernaut mistook her for one of them and tried to kill her in the name of revenge.

Aeion energy is related to the X-Parasites in some way.
SR 388 is seemingly the only planet where the Chozo have cultivated this special type of energy. It's also the only known planet that the X-Parasites are native to. The average type of X and the only ones seen in the game are yellow, just like how Aeion is represented in the game. As for Metroids, they drop/leak Aeion after counters because they eat X, but if Aeion is based on X energy and every enemy drops it when they're killed, that has some disturbing implications for every enemy you see in the game...
  • Unlikely, as in the tie-in manga, the Chozo site the X Parasite's potential to be weaponized as a reason to eradicate it.
    • There's an alternate theory that the Chozo might have accidentally created the X itself through Aeion experiments, as before the 4th Chozo Memory, the fauna of SR 388 seemed rather unharmed, with no X in sight (but we see the Chozo extracting what appears to be Aeion from the creatures there). Plus, all witnesses were seemingly killed by the rogue Chozo, so the X's nature could have been covered from the Chozo living outside Zebes, like Old Bird.
  • X being a form of Aeion corrupted by Chozo experimentation makes sense for multiple reasons. Not only does yellow X first appear in the memory immediately after the Chozo are shown conducting experiments on yellow Aeion harvested from dead hornoads, but it also explains a number of other odd things:
    • Aeion is harvested from dead bodies. If you could inject Aeion into a dead body, perhaps it would reanimate; what would happen if you injected it into a living creature, or an alien corpse from an Aeion-less planet? Would it become more vivacious than a merely living organism? Perhaps it would mutate? X shows both of these abilities.
    • X doesn’t fit in as a natural part of the SR 388 ecosystem. It doesn’t seem to run amok until the Chozo arrive, and yet we don’t know of any other creatures or environmental factors that would have kept them in check. The Chozo decision to, basically, bioengineer their own cane toad, seems much more reasonable and responsible if X only became dangerous as a result of something they did.
    • Metroids are the only creatures in the game that don’t drop Aeion when they die, but perhaps that’s just because they aren’t native (Samus doesn’t either). If X is derived from a kind of life energy, though, then that explains why Metroids - custom-designed solely for the purpose of destroying X - are also dangerous to all other life.

The Rogue Warrior Chozo were first seen in Metroid Zero Mission, and are a different race
  • In Zero Mission there are 2 different types of Chozo statues. The regular kind with the eagle-like beak we're used to, and the narrow-beaked more ancient-looking Chozo statues that hold the Unknown Items. The Warrior Chozo seen in the final image of the Chozo Memories has the same kind of narrow pointy beak as opposed to the regular curved-beaked Chozo seen in the prior Memories. Consequently, the Gravity Suit, Space Jump and Plasma Beam were creations of the Warrior Chozo, not the peaceful Chozo who raised Samus.
    • It may not be that they are a different race, but simply that they are wearing a different a different design of Power Suit. If you look closely, you can see the iconic Varia Pauldrons on the Unknown Item statues, implying that they are armored.

The X-Parasite in The Stinger becomes the SA-X
Metroid Fusion opens with Samus exploring a cave near the surface of SR388, where she kills a Hornoad-X and becomes infected by the yellow X-Parasite that is released from its form; this X goes on to become the SA-X. In Samus Returns, The Stinger shows a scene on the surface of SR388 where a yellow X infects a Hornoad and becomes a Hornoad-X. While possibly coincidental, these details (the surface, yellow X, Hornoad-X) appear to be deliberately chosen to match up with those seen in the opening of Fusion, which would indicate that this specific X happens to be the same X as the SA-X.

Ridley in Super Metroid is an X-Parasite clone.
It may be a reach but after the True Final Boss fight with Ridley, The Stinger shows one of his scattered remains before the X make their appearance. However we didn't see anything break off during the fight. Could this be because his body was consumed by the X; resulting in the fully regenerated form seen in Super Metroid? Given the history of this franchise, it's not impossible for this to occur in a hypothetical Super Metroid remake.
  • He could have just regenerated by slaughtering the inhabitants of Ceres, and obviously he doesn't become a Core-X after his death in Super.
  • We've already seen an X-Parasite clone of Ridley: Neo Ridley/Ridley-X from Fusion. It would be strange for an X-Parasite to not mutate Ridley in Super, but then mutate him later in Fusion.

The Rogue Warrior Chozo are the Space Pirates
The Rogue Warriors know the location of SR 388. The Rogue Warriors know about the Metroids, which took the Galactic Federation completely by surprise on Zebes. The Rogue Warriors in the background of the 2d/10 picture are wearing armor with more than a passing similarity to Space Pirate armor designs.

The Galactic Federation has blockaded SR-388 since the events of the first game.
That's why the Space Pirates had to rely entirely on their supply of salvaged Tallon Metroids throughout the Metroid Prime Trilogy rather than on new specimens retrieved from SR-388 (barring that single dissected SR-388 specimen found in the Metroid Processing room of Metroid Prime 3: Corruption). It's also why Ridley was the sole Space Pirate to show up and grab the Baby Metroid; having a single powerful commander slip through the blockade was easier than sending a larger and more easily detectable expedition (which would also make Ridley more of a Foil to Samus, as the same justification was used for the Federation's One Riot, One Ranger approach to the initial Zebes mission).

There was a schism between the pacifist/xenophiliac Chozo and the more extremist/xenophobic members of the Warrior Caste, and in a future game we will fight a legitimate Warrior Caste Chozo as a result.
Due to the increasingly peaceful bent of most of the Chozo, and the fact that several of them, like the Warriors in Old Bird's group, deliberately modified themselves to reduce their aggressive impulses, the more extremist Warriors split off from them in disgust. They also objected to the more extreme Aeion experiments, which was why they killed the scientists on SR-388. At some point in the future, Samus will come to their attention, and they will attack her, as she is an affront to their xenophobe sensibilities as a non-Chozo trained and taught in their culture.
  • Another idea is that the Warrior Chozo were disgusted by the SR-388 Chozo's failure to control the Metroids. They massacred them so they could take some of the Metroids for future weapons development of their own.
  • Partially confirmed by Dread; the ruthless warrior Mawkins massacred the Thoha Chozo on SR-388, but Raven Beak seizes all their research for himself so he can escalate his tribe towards conquest of the galaxy.

The Autoad enemies were created by the Chozo to fight the rebellion of the Metroids.
Based on the Chozo Memories, we can see that the Aeion energy of SR388 played a large role in the Metroids' evolution and rebellion against their Chozo creators. Since the Autoads can create an EMP-like pulse that temporarily disables Samus' Aeion Abilities, it's possible that they were created in order to suppress the power of the Aeion and keep the Metroids controllable. As we see, however, the Chozo were unable to completely stop the Aeion energy and it didn't work out in their favor.

Assuming there'll eventually be a Super Metroid remake, it will be titled "Metroid: Samus Forever".
Followed by an Other M remake titled "Metroid: Samus and Robin".

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