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. 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. 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. After boarding, Samus soon comes into contact with the Galactic Federation 07th Platoon, headed by her former commanding officer, Adam Malkovich. 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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