Bay doors are a type of security hatch used by the Galactic Federation. They appear on Bryyo in the indoor Hangar Bay Landing Site. Ships that wish to land in the hangar have to fly in through these doors, which lock when hostile intruders are detected.
When Samus comes to the Hangar Bay to upgrade her Gunship with a Missile Launcher, she is ambushed by Reptilicus Hunters and Warp Hounds before she can call in her Gunship. The ship-upgrade system retracts, and the bay doors close while Samus is forced to defeat the hostiles. Destroying them lifts the lockdown on the room, but the bay doors remain locked. Samus must engage a manual override to open them. Since the manual override is at the top of the room, Samus must scale it after using an elevator, by moving along the top of the the ship-upgrade system racks into a sealed room, where she can use a Switch to open the doors.
The doors become unscannable after they are opened, and are not scannable before they close.
"Bay doors locked shut. Unable to access landing pad. Engage manual override."