Please note that the whole point of this thread is to spoil the fuck out of everything, starting with the final boss. So if you want to play the game and experience these revelations for yourself, this is your LAST CHANCE to turn back now.
Alright, so the story generally follows Metroid II as Samus arrives on SR388, homeworld of the Metroids, on a mission of genocide. She cuts a destructive path through the population, kills the only breeding Metroid Queen, and then encounters an egg that hatches into a baby Metroid that imprints on Samus and thinks she's its mother.
Samus can't bring herself to kill THE BABY THE BABY THE BABY and so she decides to bring it back to her ship and deliver it to the Federation for study. All of this is pretty much how things went in the original.
Except this time there's a twist.
As Samus and the baby Metroid reach the surface of SR388, an unexpected foe swoops down on them intent on retreiving the only surviving Metroid. That's right, Ridley is back!
Ridley Boss Fight Video
Samus survives a brutal final battle with her old enemy, with some help from the baby Metroid who just wants to protect its mother. They fly off towards the events of Super Metroid, leaving a pacified SR388 that's now totally not dangerous at all.
Wrong, because we then cut to a chilling after credits scene.
Post Credits Video
Yes, that is an X Parasite taking over an alien. As we learned from the events of Metroid Fusion, the X Parasites were the original scourge of SR388 and a threat to the entire galaxy. These creatures were so dangerous that the benevolent Chozo (who raised Samus) actually created the Metroids to serve as a natural predator that could keep them in check.
The annihilation of the Metroid species led directly to the recovery of the X Parasites and the events of Metroid Fusion. We know now that MercurySteam originally pitched a Metroid Fusion remake to Sakamoto. Could this be foreshadowing their original plans?
Originally Posted by Metroid Fusion
The creature took on the host's memories, appearance, abilities, everything. It sucks everything dry. Utterly terrifying. Can you not see that if a mimic such as this were to infiltrate a population, it could replicate almost indefinitely! With evil taking the form of an ally, the galaxy could be overthrown. It is truly the worst kind of evil... it has no name, but... we call it X.
I would say that the evidence so far suggests that, but then for players who clear 100% of Samus Returns we get something even more cryptic that might hint at something else entirely. Here are a series of images that seem to tell a story; some of it we know already, but the rest...
Here we have the Chozo arriving on SR388. Note the three key figures here and their distinguishing features. They're clearly Chozo leaders.
The Chozo are extracting X Parasites from their hosts. Studying and analyzing the threat.
An attempt to exterminate the X Parasites through conventional means? They appear to be scanning life forms for signs of infection.
That's a lot of X Parasites. Presumably the nasty critters did not want to go quietly into the dark night.
Designing the Metroid. When faced with a galaxy ending threat, just make something bad enough to feed on it. What could go wrong?
Everything is going according to plan.
Success! No more parasites. Let's pat ourselves on our avian backs.
Holy shit our own creations are mutating out of control. Who would've thought?
Alright so clearly everything is just fucked now. Time to flood this place I guess? And let's get the fuck out of here.
Now here's the really interesting part. We have the two (remaining?) Chozo leaders arguing about something. These appear to be the same guys we've seen in most of the other images. Maybe they're arguing over whose fault it was, maybe they're arguing over the future of the Chozo race, maybe they're arguing over whose turn it was to do the dishes.
And now there's only one Chozo leader left. He's standing in a kind of tyrannical pose, with a smoking gun on his arm, and a bunch of dead Chozo at his feet including the guy he was politely debating. The red is not ominous at all.
So to me the implications here are clear. As far as I am aware, the fate of the Chozo race has never been specifically stated anywhere in the Metroid series. We know they explored the galaxy, we know they left lots of ruins and high technology, and we know they adopted Samus and gave her the Varia Suit. And we know they've just been kind of gone.
To this day we've never seen a live Chozo in a Metroid game.
People speculated they might've been wiped out by Metroids, by X Parasites, by Space Pirates. But it wasn't any of those, was it? This new evidence seems to tell us that it was actually a Chozo civil war that ended with an "evil" faction taking control. This faction and its leader were directly involved in the creation of the Metroids.
Where are they now? What have they been up to?
Spoiler: Whatever it is it probably involves making new Metroids.
Could the answer to those questions be the basis of Metroid 5?