Game: Metroid
What Makes Her Bad: An AI created by the Chozo who wants to "reset" the universe.
What Makes Her Cool: Mother Brain is actually a brain. With an eyeball. Check her out.

When the Chozo created Mother Brain, they couldn't have known what a pain she'd end up being. After the Space Pirates invaded Zebes, she found true potential within them, and figured that if she could turn them over to her line of thinking, together they could "reset" the universe.