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I feel like this more sympathetic tone towards them could have made Ridley’s appearance in Metroid: Samus Returns a bit more impactful by having him be a sort of narrative symbolism for the use and abuse of the Metroids by higher powers who wanted to play god. Maybe start the game with Samus delving into the desolate, barren husk of a landscape that is SR388. The planet is cold and dead on the outside, dust fluttering about in the wind, harkening back to all the dry, lifeless bodies left behind in the wake of the rampaging Metroids we’ve seen throughout the series. As she delves deeper into the underground cave networks, it becomes clear that, while many have become terrifying, dangerous predators, there is an ecosystem that some that aren’t Ridley may call beautiful. There are creatures that take on different roles in the food chain, with different mutations of Metroids having many different roles in this natural, albeit highly competitive, web of life.
Maybe have some monologues about the tragedy of it all. The capabilities of these creatures are sure to be exploited if ill-intentioned people acquire them, and moving an entire, dangerous ecosystem off world simply not be feasible for a simple Bounty Hunter, even one of such renown as Samus Aran. It’s a very unique dilemma to explore. Either kill an entire ecosystem of innocent creatures, or let them live and possibly end up with your inaction causing hundreds, even thousands of deaths in the long run, all passing on in incredible agony.
Then, all is said and done. An entire biological order has been wiped from existence. The Queen Metroid, which spawned all this blooming life like a goddess of creation, has been slain. With her gone, the possibility of an ecosystem of this type is gone forever. But one Metroid remains. A single, lone hatchling, oblivious to all of Samus’s terrible deeds on this world, innocent and friendly. The possibility still remains. The Space Pirates have already succeeded in asexually multiplying Metroids to orders of magnitude of their original supplies in the past. This one single specimen could make a legion if it falls into the wrong hands.
But this is a child. A lone child, without its mother, sitting in an afterglow of ash and death, with none of its kind left for hundreds of light years. It looks up hopefully to a stoic, alien figure, sigils in its technology baring the mark of the Chozo. Quite familiar, no?
As Samus and the last child of the Metroids leave this barren waste behind, she believes that maybe some good can come of this. If nothing else, she has done some small favor for this weary conscience of her’s.
Then, who else should show to complete the metaphor but the Cunning God of Death himself? Contrasting Samus’s gentle approach with the baby Metroid, Ridley is brutal, shrieking alien obscenities at this frightened child, beating it into submission as it fights back against his taloned grasp. This is the face of heartless control and abuse, this is the face of those who made the Metroids an enemy to life in the galaxy. They used these animals to commit atrocities, like throwing the condemned to a pack of starved wolves. This is what playing god looks like. And now the Hunter must cut him down to size.
Really nice thing about Metroid as a series? The Metroids themselves are both presented as incredibly terrifying creatures with the after-effects of their lifeforce draining being showcased disturbingly, particularly in Super Metroid and Prime 3 (GFS Valhalla, anyone?) yet the overall narrative framing of them still makes it pretty clear that nothing in the series is really their fault, the danger they pose is entirely due to outside factors like the Space Pirates and Phazon. Even though them starting to show up in any given game is usually a sign that you're entering The Hard Part, they're still just creatures at the end of the day and treated very sympathetically; Space Pirates abusing them is specifically called out in some of the Prime 2 scan entries.