The ultimate form of Mother Brain. When Mother Brain was destroyed during Samus's first mission, Samus unknowingly missed a hidden backup located beneath the original. This backup was rebooted shortly after Samus left Zebes, and began to slowly recuperate from her losses. Once she was able to gain full control back over the Space Pirates and the creatures of Zebes, Mother Brain was rebuilt more powerful than ever, and given a fully mobile "body" which allowed her to tower over Samus.
Samus was no match for this version, as Mother Brain knew exactly how much firepower it would take to defeat her. Mother Brain's Hyper Beam almost completely killed Samus, but was saved just in the nick of time by the former Baby; now mutated into a Super Metroid.
The Super Metroid sucked Mother Brain's extra power dry, and used it to bring Samus back from the brink of death. Mother Brain was not completely defeated, however, and when she awoke, she destroyed the Super Metroid. The remains of the Super Metroid fell onto Samus, resulting in the transferal of the Hyper Beam to her, giving her the added weapon capacity to destroy Mother Brain once and for all.
