The System Management room is a room in the Main Sector. It controls the electrical systems throughout the BOTTLE SHIP. It is deactivated when Samus Aran and the Galactic Federation 07th Platoon touch down on the ship, but Samus is ordered by Adam to reactivate it after the fight with the Brug Mass. Before she can do this however, she must destroy two Fly Pods spawning Reos. The door to the System Management room possesses a unique design different from the regular Main Sector doors and all other doors on the ship. This door also contains a small glass window that allows Samus to look through into the corridor beyond.

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