Once Samus has the upgrade, she is ambushed by Security Robot B.O.X., and Samus heavily damages it, but it escapes before Samus can destroy it.

Samus defeats it and is directed to Sector 3 to obtain the Super Missile upgrade because the SA-X has inhibited access to the closest Data Room (Sector 2). Through exploration, Samus discovers that Serris is dead, and that the actual culprit is an X copy. Because of her weakness to cold and the SA-X's possession of the Ice Beam, Samus is instructed to avoid it, and after receiving the Bomb upgrade, Samus travels to Sector 4 to investigate reports of damage, which Samus's ship computer attributes to Serris, a fast-moving, snake-like organism whose rampage has severed some power nodes and electrified pools of water throughout the sector. It is also the source of the explosion in the Quarantine Bay. The computer on Samus's ship then detects a disturbance in Sector 2, the presence of X Parasites, and once there, Samus learns of the existence of the SA-X, an X Parasite that has adopted her form and has all of her weaponry at its disposal. In Sector 1, after learning that the Main Elevator has been damaged by an unknown source, and X have been released into the sector, Samus rectifies an atmospheric irregularity after some X hijack the sector's five environmental stabilizers in order to suit their needs. During the trip, the X multiply inside Samus's body, severely endangering her life. employees discover the pod and send it to Galactic Federation headquarters. She is ejected via an escape pod, and the ship crashes into a nearby asteroid belt. Research Station, her central nervous system is compromised, causing her to lose consciousness and control of her ship. However, upon its defeat, the Hornoad turns into an unknown, amorphous organism known as an X Parasite, which immediately infects Samus. While exploring an underground cavern, Samus encounters a Hornoad and dispatches it with a Missile. Sometime after her return from the Bottle Ship, Samus is sent to SR388 to protect a group of Biologic Space Labs Research Station employees who are studying the planet's life-forms now that the Metroid population has been exterminated.

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