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As the heart of the operations, the Zebesian Command Center was under heavy guard. Cannons and Rinkas fired around this room and in previous rooms to ward off intruders, and Zebetites holding together walls in the room served as blockages. The floor in the section of the room where Mother Brain was accessible contained lava in Metroid and Zero Mission; in Super Metroid a more potent lava that could harm through the Gravity Suit rose to fill the entire room. Samus Aran destroyed Mother Brain twice in this room, and immediately after her deaths countdown sequences began, forcing Samus to escape.
In Zero Mission, returning to the destroyed Command Center reveals that it has since been flooded by Beta Acid, a green substance that is corrosive enough to harm Samus with the Gravity Suit active. Samus returns through here when she returns to Zebes in search of the baby. After descending to Brinstar and returning, Samus finds that the Space Pirates have appeared and now know she is on the planet.
Samus enters a rebuilt Command Center later in Super Metroid and once again must destroy Mother Brain. As stated, the room was filled with a potent lava that could harm Samus even in the Gravity Suit. After Samus seemingly destroys Mother Brain, her Control Capsule explodes, as does the platform on which it is situated, and she and Samus are locked into a smaller room. Mother Brain then attaches herself to a large mechanized body and nearly kills Samus. Before she can strike the finishing blow, the baby appears and siphons Mother Brain's energy, transferring it to Samus. Mother Brain rises again a few moments later and destroys the baby over Samus. Samus uses the power of the Hyper Beam granted to her by the baby to kill Mother Brain. Another countdown triggers, this time to destroy the entire planet of Zebes. The wall in the back of this chamber explodes, allowing Samus to escape.
- 15 in Metroid
- 12 in Zero Mission
- 13 in Super Metroid
- 5 in Metroid
- 4 in Zero Mission
- 6 in Super Metroid (two large Zebetites and two sets of two smaller Zebetites)
- 5 Zebesians (Super Metroid, destroyed Command Center)
- Missile Tank
- Super Metroid. Bombing the floor under Mother Brain's former location reveals a chamber Samus can drop into, at the bottom of which is this Tank.
- Power Bomb Tank
- Zero Mission. Once again under Mother Brain's resting place, requiring a Super Missile to break through a block.
- The Metroid Prime 3: Corruption Preview trailers feature blueprints for a Future Aurora Complex that is identical to the Zebesian Command Center in Super Metroid.