Metroid Database.com

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1. How do I defeat the boss that rolls up into a ball?
   
   Answer:
   This is the monster known as Arachnus. Since your shots and missiles aren't hurting it, what other weaponry do you have? Take a hint from the Archnus itself and try the weapon you can use when Samus rolls up into ball form. Um...that'd be the bombs, of course. Your reward for defeating Archnus is the Spring Ball.
2. How do I defeat the Queen Metroid?
   
   Answer:
   The Queen attacks with flying shots and by extending her neck and snapping at Samus with her sharp teeth. Jump and use the Screw Attack to avoid and/or go through the shots. Stand in the lower right corner, facing the Queen, and when she snaps at you, fire a missile into her open mouth. Missiles fired at her head will damage her at any time, but if you fire a missile directly into her open mouth when she's attacking, she will freeze momentarily. Take this opportunity to unload more missiles into her head -- sometimes you can make her freeze 2-3 times in one attack. Another method is to make her freeze with a missile to the mouth, then turn into a ball and roll right into her mouth. When the Queen retracts her head, Samus can roll into the Queen's belly and lay a whole bunch of bombs, doing quite a bit of damage, until the Queen barfs Samus back out. (This does, however, take energy away from Samus as well.) Repeat and/or combine these techniques until the Queen Metroid croaks. And remember, if Samus runs low on energy or missiles, she can roll out the small passageway at the bottom of the room to refill, but then she must make her way back to the Queen's room for another round. Good luck!