After Samus saves the Platoon from the Brug Mass,Adam allows her to cooperate in their mission,under the condition that she follow his orders. On her journey through the tropical area,Samus encounters 3 small furry creatures. She went to the Exam Center where she and the Platoon discovers that the BOTTLE SHIP was to conduct research on bioweapons,a practice that is illegal within the Federation. They learn the person in charge was Bergman. The Platoon are attacked by 3 large lizard-like creatures. Samus and Anthony manage to blast them before the Creatures escape. She discovers the skins of little creatures and follows them.
Samus finds the bodies of two Platoons,Lyle Smithsonian and Maurice Favreau. She even sees a young woman,who introduced herself as Madeline Bergman. She explains that the scientists has collected Metroid Eggs and studies them. They even study the little creatures. They were both had to be controlled by an AI named MB. Samus soon realized that there's a traitor among the Platoon and has killed Lyle and Maurice. They were both ambushed by Alpha Metroids,but quickly escapes to the Bioweapon Research Center. Samus goes to the Sector Zero where MB and the Metroids were stored. Madeline is approached by the traitor also called the Deleter,who shoots her.
On the way,Samus notice the husks of three Creatures she follows and helps Anthony and the other Platoon member,K.G. Misawa fight off the Gamma Metroid and Zeta Metroid. After the Gamma gets taken down,the Zeta gets killed by 3 Winged Monsters,who turned out to be the Ridleys. K.G was killed. Samus manage to take out one of Ridleys by blowing one of his wings,causing him to fell into the lava. The two escape,but not before Anthony gets knocked off the Platform.
Samus arrives at Sector Zero where she encounters a Baby Metroid. Before she can kill it,She is struck from behind,disabling her Power Suit. It turned out to be Adam,who kills the Metroid just as quickly. He states that his intention to enter Sector Zero and to destroy it,he explains that,by causing enough damage to the sector,it will detach from the ship self-destruct,thus destroying MB and the Metroids. Before sacrificing himself,Adam commands Samus to secure a survivor in Room MW.
After Samus manage to blow another Ridley into space,She returns to the research center to find the body of the Deleter,James Pierce and the mummified remains of the last Ridley. She finds a survivor,who reveals herself to be the real Madeline. She tells her that the Madeline she met was MB,an android created from Mother Brain. She has created the cloned Ridleys from the remains of the real one Samus killed. They were confronted by MB,who has released the Queen Metroid. Before the Queen try to kill Samus,the ship's emergency brakes went active,allowing Samus kill the monster with a Power Bomb in the stomach.
Madeline shoots MB with an ice cannon before the Federation Troopers,who rushed in,open fire,finishing her off. The Colonel compliments Samus' efforts but orders a soldier to escort Samus back to her ship. The soldier reveals himself as Anthony,who has survived the fall. As Samus,Anthony,and Madeline leaves in Samus' Gunship,Anthony shows her two things while looking for her: Adam's Helmet and a Metroid Egg.
Mid-Credits:
In the Facility,Ganondorf approaches Ridley. The R.O.B.s inform him that they found him in space. Ridley open his eyes,revealing to be alive.