Future Aurora Complex

Metroid Prime 3: Corruption Preview trailers depicted blueprints for a Future Aurora Complex. While meant to be taken as blueprints for an Aurora Unit chamber, it is very worthy to note that the blueprints depict a room identical to the chamber of Mother Brain in Super Metroid. This could mean that the Space Pirates stole these blueprints and used them in the reconstruction of the base.

Mother Brain's chamber
Mother Brain appears in her own chamber in Metroid, Super Metroid and Metroid: Zero Mission. The chamber is always a long corridor initially, divided into small sections by pipes. Between these pipes are the tissue that serve as Mother Brain's life support, Zebetite. These must be destroyed to continue, but should firing Missiles at them cease for a while, the Zebetites will gradually regenerate. They do not return once destroyed, however. Once the Zebetites are destroyed, Samus can jump through the gap left by them, either in bipedal or Morph Ball form. It is curious to note that if a pipe has two separate gaps for Zebetites that Samus will have to roll through, firing at one Zebetite and destroying it will shrink and destroy the other as well, suggesting the two are somehow linked. The room's floor is always submerged in magma. In Metroid and Zero Mission, the magma is always here, but in Super Metroid the magma rises in the room with an earthquake. In the former two games, because Samus does not have the Gravity Suit the magma can damage her. The magma present in Super Metroid is a superheated variant that even the Gravity Suit cannot withstand, present in Ridley's Lair and previous rooms in Tourian as well. Interesting to note is that in Metroid, after Mother Brain is killed the magma turns white and is rendered inert.

During the Mother Brain fight, Rinkas and Cannons attempt to impede Samus' progress. These can be a nuisance when Samus finally gets to the Control Capsule and begins firing at it. In Zero Mission, Samus is sealed into Mother Brain's section during the fight, but not in the original game. When Mother Brain falls to the ground in Super Metroid after taking enough damage, she and Samus are boxed into a small area where they battle, Mother Brain being assisted by a mechanical body. Somehow the baby is able to enter this area and drain the Mother, then restore Samus before it is killed. Metroid: Other M depicts a larger version of this room, appearing less constrained (which may be due to Mother Brain's increased size in the introduction's flashback). Samus seems trapped in here as the Countdown begins in Super Metroid, but the back wall explodes and leads to a small corridor with closing shutters, which Samus can destroy with her newly-acquired Hyper Beam. The original game had her run past Mother Brain's remains to a tall shaft with small platforms (made of Pit Blocks in Zero Mission), at the top of which was an elevator out of the exploding Tourian base (in Metroid this brought up the ending screen, but in Zero Mission the escape is extended to include part of Crateria). In Super Metroid, Samus enters the ruined original shaft while escaping from the new Tourian, and is forced to climb it once again. If she is able to charge a boost from the last room, she can Shinespark up the shaft to a certain platform, where she will stop. The superheated magma rises in this room.

Samus can return to the original chamber after its destruction in Super Metroid and Zero Mission. The chamber is quite obviously wrecked due to the Time Bomb explosion, and there are even some powerups that Samus can collect. Both games give Samus the ability to destroy the floor where Mother Brain was to fall into an underchamber (foreshadowing her body) containing an expansion (Missile Tank in Super and Power Bomb Tank in Zero Mission). In Super Metroid the ruined Tourian is grey and bleak, in Zero Mission the wrecked area is colored a dark purple and has an appearance of acid erosion. Zero Mission also features the presence of a strange blue-green liquid that can damage the Gravity Suit, which Samus would again encounter in the Tourian-like area of Sector 1, an area created to propagate Metroids, though unlike the Sector Zero of the Bottle Ship, it was not known to contain a Mother Brain-like computer to control the Metroids with its brainwaves.

Trivia

 * Though Sector Zero was never actively seen, it is possible that the Galactic Federation used the blueprints to make the brain MB’s chamber.
 * The chamber also appears in WarioWare microgames re-enacting the Mother Brain fight in the first Metroid.
 * In the first Metroid game's map, the Mother Brain chamber is shown to be directly above the very first room in the game, the Brinstar entry point.
 * The Mother Brain chamber is the only room in Metroid and Zero Mission to play the Zebetite theme.