In my opinion, environmental ecology is one of the most under-exploited narrative themes in the Metroid series. As a whole, Samus's recurring role has been to protect different planetary environments and civilizations from the threat of ecological demise - whether it be from Metroid and X-parasite infestations, Space Pirates exploiting planetary resources and polluting the environment with Phazon, or Ing dominating ancient civilizations via dimensional rifts. I think the Metroid series could use its plot devices to construct more intentional story lines that play off the real-world problems of environmental imbalance, pollution, resource exhaustion and the disenfranchisement of marginalized cultures in a complex global economy.
There is also extraordinary potential to create stronger character identities and motivations within these adapted real-world conflicts. Rather than just having the same-old duality of "good" vs "evil" - we could get a bigger, more empathetic Metroid world by opening up difficult anthropological problems that affect character's motivations in both positive and negative ways. In a more complex ecological narrative, one might ask: does Ridley have a good side? Or, why is Samus trying to preserve one civilization, yet destroy another? As Samus, the player could experience contradictory/teachable moments that make them question their own morality. Furthermore, I think Metroid's traditionally non-linear game design would be a great way to implement a this type of narrative theme. Players could explore environments, as well as different narrative elements.
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