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I think few villains/bosses will reach the emotional feel of Mother Brain in Super Metroid. The shock when she changes form would be reason enough for me to put her on the list. The feeling of despair/frustration when she takes you to near death is horrific. I'm not going to reveal the bit of deus ex machina that appears after this moment...but it really completes your transformation into a god-like being when you already felt indestructible. The moment is so iconic, it probably is the best thing about Metroid: Other M.