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Samus leaves the Pyrosphere and witnesses an unknown soldier (most likely the Deleter) entering the elevator to the Biosphere. Misawa is incinerated in an unknown area of the sector. Contact with Adam is also inexplicably severed, and K.G. Samus later encounters Ridley in the Geothermal Power Plant, and Anthony is seemingly killed. Returning to the Pyrosphere, Samus saves Anthony from the Rhedogian (first encountered on an elevator while leaving the Cryosphere) and, possessing conflicting feelings about Adam, remembers the events leading to death of Adam's younger brother, Ian Malkovich. Samus calls this unknown assailant the Deleter. Samus is sent to the Pyrosphere in pursuit of this creature, but she is quickly directed to the Cryosphere, where she finds the body of Maurice Favreau and is attacked by the RB176 Ferrocrusher while in pursuit of an unidentified woman, who claims that Maurice was killed by another soldier. They are then distracted by a mysterious, reptilian creature, which assaults Samus before being repelled by Anthony Higgs and escaping. Samus and the platoon learn that the Bottle Ship is operated by the Galactic Federation and was designed for the propagation of bioweapons.
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Before this, however, she encounters the body of another scientist (found in the Biosphere's Breeding Room) and a peculiar bird-like creature. Samus rendezvous with the platoon in the Exam Center, located in the Biosphere Test Area. The platoon is then briefed, and exploration of the facility begins.
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The Brug Mass is engaged shortly thereafter, and upon its defeat, Adam allows Samus to offer the platoon aid under the stipulation that she follow his orders. Samus meets up with them in the Main Sector's Control Room, where they find the corpse of a scientist. Samus tries to discern their reason for boarding, and she, as an "outsider," is denied this information, and the platoon moves on ahead.
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After boarding, Samus soon comes into contact with the Galactic Federation 07th Platoon, headed by her former commanding officer, Adam Malkovich.
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Sometime later, she receives a distress signal known as "Baby's Cry" from a decommissioned vessel later identified as the Bottle Ship. She then reports the results of her mission and presumably leaves. She awakes in a Galactic Federation facility and is directed to a training room by a quarantine officer, where he tests her various abilities. The story begins with Samus reminiscing about her previous mission, particularly her confrontation on Zebes with the mechanical monstrosity Mother Brain.
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