Some time after the events of Fusion, Samus' life has gone downhill, one day she happens to stumble upon one of her dad's old friends who tries to cheer Samus to recruit her for a special mission, she refuses at first but eventually he convinces her.
After a quick trip to the ancient Chozo planet and getting back her Power Suit which she had left there after Other M, Samus suits up with a brand new Zero Suit with a special oxygen device and Jet Heels. Once she's ready, she travels with her dad's friend, who's name is "Tyson", and he explains that a man and a special laboratory group went on an expedition to a planet, the man in charge of the expedition, "Dr. Terielle", was revealed to be doing experiments on Metroids to mutate them and control them, but the mutated Metroids, who were given the name "Mutatroids" went berserk and escaped. Samus lands on the planet and is tasked with rescuing the rest of the expedition team, as well as a team of soldiers who tried to stop the Mutatroids on their own.
When Samus arrives at the surface of "Planet Askhabaz" she's send by Tyson into the caves where she finds the first few Mutatroids and a group of soldiers who wanted to stop the Mutatroids until getting lost on the cave, Samus helps them out but is stopped by Trace, who has been paid by Dr. Terielle to make sure that no one finds out about the outbreak. Samus escapes and takes the guards deeper into the caves where they hide until Samus goes out to find upgrades left by other exploration teams, eventually finding a Power Missile which she uses to fight Trace and make him run away.
The game lets you switch between Zero Suit and Power Suit mode, when you're in Zero Suit, Samus becomes much more acrobatic and agile an gets the ability to use her laser whip, laser gun and Jet Heels, but once you're in Power Suit, Samus becomes slightly less agile but more resistant and her attacks focus more on the use of her Blast Gun.
The game's camera is usually behind Samus' back since the game focuses slightly more on action, but still mantains a bit of the exploration and even some of the horror elements past games had. However, the camera can be switched to first person while on Power Suit to aim your shots better or scout the area with the simple press of a button.
The game is way more non-linear compared to Other M, allowing you to explore the planet of "Neneether" to its full extent, however, just like many old Metroid games, some areas may require you to progress in the story or to get a certain upgrade in order to procceed.