Video Game Villains WarWhen Kerrigan and her Zerg forces land on the Space Pirate planet of Zebes, Mother Brain sends her forces against the Zerg. The forces reach a standstill, with Kerrigan and Mother Brain going head to head. Mother Brain unleashes her hyper-beam, severely injuring Kerrigan. As Mother Brain charges up another shot, Kerrigan rears back up and emits a massive amount of psionic energy. The force of the energy causes Mother Brain to explode.
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Mother Brain was created long ago, before the unification of Videoland states. She was created by a race of powerful, hyperintelligent aliens, known as Chozo, to work as an intelligent AI. However, with her having too much sentience, she turned evil and killed the entire race of Chozo by turning their technology against them. After omniciding the Chozo race, she started building a portal system, similar to the one in Palace of Power, which would let her conquer other realms in Videoland with her army of space monsters, and technological remains of Chozo machines.
This plan was heard by the spies of King Charles, who sent a bounty hunter named Samus Aran after her. She explored the planet, facing off against several monsters, destroying the machines and stealing powerups which Mother Brain had planned to use for her own purposes. Samus faced off against Mother Brain, shutting off her connection to the Zebes. However, she didn't know Mother Brain had a spare plan in case this would happen, and made it so that Zebes would explode if Mother Brain were to be disconnected from Zebes's central laboratory. Samus successfully escaped, but Zebes was no more. She presumed that Mother Brain had died in the explosion, but she was wrong...
Mother Brain ended up launching her chamber to space shortly before the planet exploded, this chamber was brain-shaped massive floating object, and ended up being renamed to Evil Land of Metroid. Mother Brain had a plan to overthrow King Charles and take over Videoland. Several years later, she launched an attack to the outskirts of Palace of Power with an army led by her two new allies, Eggplant Wizard, an evicted sorceror from Mount Icarus, and King Hippo, dim but strong boxer from Punch Out Land. They successfully stormed past King Charles' defenses, and cornered him.
Charles was brought into Metroid, where Mother Brain told him to surrender all power to her, or else she will do something unthinkable to him. Charles however refused, and suddenly, Samus Aran attacked Metroid with her ship. Just then, a strange zap shut down Samus's ship, and she crashed in Metroid. Mother Brain was happy to have two victims for her latest plan, and unveiled her new ally, the evil wizard Ganon. Ganon used his magic to zap Samus and Charles inside a mirror, sending them to Mirror World.
Knowing that Charles's daughter, Princess Lana was still around inside the castle, she sent her forces to patrol the castle. Lana and her helpers, Kid Icarus, Megaman and Simon Belmont, all needed a hero to save them from the trouble or Mother Brain would win. She ended up using the Ultimate Warpzone to summon a hero from real world, Kevin Keene. With the help of newly-christened Captain N, N-Team successfully drove off Mother Brain's forces.
Mother Brain was angry that her plan's second step had failed, but she didn't want to give up yet. She sent Eggplant Wizard and King Hippo to new realms that she had discovered, Mushroom Kingdom and Kongo Bongo Island, to get new allies for her. The Videoland Villains were about to be formed...