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When you get to the brain, it will start shooting stuff at you. I stand there for a moment and when it starts to shoot, I jump and shoot its head. You have to keep doing this until the cut scene appears. After that it will suck you dry of your health, but your Metroid friend will come save you. Then you get the rainbow gun and you have to do the same thing again. It takes a while to figure out the pattern for dodging the fire, but if you wait for him to shoot at your current position, you can jump to avoid it. When you finally kill the brain, you then have to run all the way back to the beginning of the game. You can go to gamefaqs.com to find a complete walk through.

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Q: How do you beat mother brain in super Metroid?
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