The Main Storyline Plot of Metroid: Samus Returns remains identical to that of the Game Boy Original. Since her last successful mission, Samus is now sent to the world of the Metroids on SR388. Here, she is tasked with duties of discovering what exactly happened to the Galactic Federal Special Squadron that was originally sent to the planet. She is also sent with a secondary, more clear responsibility: eliminate and eradicate the entire Metroid Species.
Even though the species are plentiful on this planet, this doesn't pose much threat at first to Samus and her high-tech suit. However, as she continues to progress through the planet and swarms of enemies, Samus will come across more evolved and higher advanced versions of Metroids. Harder and harder the Metroids will become, ultimately leading Samus to the Queen of this race.
The Metroids will give Samus well enough reasons as to why they must be destroyed, but a surprising twist is left to be told, one that might just make a hundred percent annihilation of the species tougher than Samus could've ever imagined. And even then, the Metroids might not be the only creatures Samus will have to defeat...