Mother Brain (true form)
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.
Fortunately, Mother Brain is one of the easiest boss battles in the game. If Samus has enough Super Missiles, you can stand right underneath of her head, aim straight up, and shoot as many Super Missiles and Missiles as you have in your inventory. Be sure to jump over the grenades she spews that roll on the ground; their explosive wake can damage Samus greatly.
When she reaches a certain level of health, Mother Brain will lean back, which makes you unable to shoot her from underneath. She will then pump out orange beams at Samus, which lock on to her location. The orange beams are easy to predict and can be avoided by jumping out of the way. Run to the bottom right corner of the room, and begin to aim directly at her head and shoot everything you can. If you run out of Super/Normal Missiles, just use charged Plasma-Wave-Ice Beam Shots. Mother Brain will then begin to charge up her Hyper Beam, which is undodgeable. If you have enough energy, Mother Brain will not completely kill Samus and the Super Metroid will save you at the last minute. You're on your own for the rest. Good luck!
Once you have Power Bombs, you can go back into Old Tourian and bomb Mother Brain's old chamber, which reveals a backup chamber underneath. There is also a Missile upgrade in here. This hidden chamber is also accessible in Zero Mission.