Since way back when, my headcanon spanning the games from Metroid to Super Metroid has been that Samus operates in a universe where non-human intelligence is mostly of a "not intelligence as we would recognize it" form. We are assured in vague terms, for example, that the "Space Pirates" have a form of cunning and agency, but their behavior in game is inscrutable and zombie-like. Zebes and SR388 are planets with a strange mixture of "natural" seeming hazards and architecture, with functioning machinery. So what if many (most?) of the mobs toodling around in those games are participants in some sort of hive mind, if not intelligent beings unto themselves? What if Brinstar and Norfair are not ruins, but thriving, living metropoli and home to full-fledged cultures with which Samus, as a human interloper, has zero ability to communicate, or interest in doing so? What if Samus isn't a sympathetic actor?
This effectively recasts the first three Metroid games as a sort of Rampage clone, in which Samus is at times an accomplice to, and at other times a principal agent of, overt, totalizing xenocide. Ridley and Kraid, then, might be something akin to warlords, or perhaps represent members of a "ruling caste" in their respective hive minds. This would reconcile Ridley's characterization as "shrieking gargoyle" with his reputation as a pirate extraordinaire - the player is afforded no opportunity to engage with or even recognize that intelligence, since Samus simply storms into Ridley's office like Agent 47 executing a CEO and Ridley's got little choice but to defend himself. This is not to say Ridley's a goodie either (they are, we are assured, pirates, so maybe this is just one of those War Never Changes sort of situations), but the inhumanity of Metroid's foes, the impossibility of establishing empathy for them, feels deliberate.
This lens casts the ending of Super Metroid in particular as almost unspeakably bleak (although it has always been considerably darker than most fans seem to realize; even if you deny most of Super Metroid's mobs any meaningful sentience, the destruction of a planet is an irreplaceable loss). To be clear, this doesn't take anything away from Super Metroid, which I consider to be as close to a perfect game as was released on the SNES. It's also not terribly original (no doubt the earliest video game webcomics in existence lament how Mario is mass-murdering his way to Bowser's castle), but it's not an angle I've seen others adopt about this franchise in particular.
Obviously, this is a private interpretation, and not one that can be reconciled with the much more elaborate and specific textual world-building of later games. I doubt it can even be reconciled with the game manuals that those three games shipped with (which I certainly didn't read closely, or maybe even at all, despite buying all three games new). It's more a way for me to reconcile Samus' grim "faceless, unrelenting exterminator" vibes with the game's casual assumption that, as protagonist, she is heroic by default. It wouldn't be until I played Shadow of the Colossus years later that I experience a game textually and thematically grapple with the "main character syndrome" hubris of systematically cutting down all who came in their path, but Super Metroid felt sad to me in a way that didn't fully click until SotC made that theme impossible to ignore.
