Samus received a distress signal going on at the Bottle Ship. Soon after landing,Samus encounters the Galactic Federation 07th Platoon, among them are Anthony Higgs,an old friend from her military career,& her commanding officer Adam Malkovich. After Samus saves the Platoon from the Brug Mass,Adam allows Samus to cooperate in their mission, under the condition that she follow his orders.
Samus & the Platoon investigates around the ship. She encounters three little creatures. They discover that the person in charge of the project is Madeline Bergman. They are both attacked by 3 large lizard-like creatures. After defeating them,Samus is ordered to pursue them. Samus found two Platoon members,Lyle & Maurice dead.
She pursues the creatures at the Pyrosphere,Where She,Anthony, & Misawa are attacked by three Creatures,who turned out to be the Juvenile stage of the dragon-like Ridley. Misawa was killed & Anthony was knocked over. Samus killed one,but the two escaped. Samus found the woman at the Bioweapon Research Center. The Woman introduced herself as Madeline Bergman,who saw the member of the Platoon killed the two. She reveals that all the Metroids had been captured so they be studied under the control of MB,an artificial intelligence & three Ridleys are cloned from one Samus killed. She follows the Metroids to Sector Zero,but Adam stops her from entering & explains why the operation should not be attempted due to potential dangers. He states his intention to enter Sector Zero & to destroy it,the Sector will receive damage before it can be detach from the Bottle Ship & self-destruct. Before sacrificing himself,Adam commands Samus to secure a survivor in Room MW of the Bioweapon Research Center.
After Samus blasting the second Ridley into space,She returns to the research center where she finds a mummified remains of the last Ridley. Samus finds a survivor & is confronted by the Platoon's murderer,who turned out to be James. The Metroid Queen appears & kills James. After Samus kills her,She pursues the survivor,who turned out to be the real Madeline Bergman. She explains that the woman she met was MB,an android that was created & had been corrupted by Mother Brain.
They are soon confronted by MB,who summoned all reptilian like Metroids. After Samus took down those creatures,MB gets frozen with an ice cannon by Madeline before getting finished off by the Federation Troopers,who rushed in the room. The Colonel compliments Samus' efforts but orders a soldier to escort her back to the ship. The soldier reveals himself as Anthony,who survived Ridley's attack. Samus,Anthony,& Madeline leave for Galactic Federation headquarters. Anthony shows her two things he found while looking for her: one is Adam's helmet & a Metroid Egg.
Mid-Credits:
Ganondorf & Bowser are informed that Ridley was found,drifted into space,alive.