Metroid is one of those franchises with a sort of blank canvas for a background story. We know Samus is a bounty hunter, pirates are evil, and Samus kills a lot of stuff while powering up to advance progress.
The very little stroy that Metroid has is GREATLY influenced by one of the greatest films ever made
If you take the human interaction out of Alien and have the Metroids reproduce/morph with the pirates and planets animals instead of the Xenomorphs with humans, you have a grade A movie. All you need to add is a flashback with Samus being raised by Chozu, a final fight with Mother brain where Samus should use her mega beam, after she should turn into Zero Suit Samus for an exciting escape from a self destruct sequence while also avoiding/fighting Ridley, and some powerups introduced periodically to help samus advance.
Make the colorschange in Samus suit as she upgrades for hardcore fans, peiodically show us a visor view when she scans monsters, Nintendo produced music because no one could do it better, and creepy isolation to make the film as game/Alien-like as possible and you got a 100% crowd pleaser.
Find a way to work in the baby metroid saving your life while you escape from Ridley/self-destruction sequence and the computer that has a thing for you from Metroid Fusion (maybe make it her ships computer that communicates with her) and you might get academy awards. If someone finds a way to mess this up they should be made into a ball like samus and thrown in a bucket with jellyfish.