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Fighting the bosses
The best way to defeat the Dragondroid is with a charged up atomic fire and several little blasts afterwards. You'll destroy hi in a hurry.
The best weapons to use in the stages, not the Dr. Wily Skull Castle are
Bubble Man: Metal Blade (4 hits) Tip: Don't jump too high and just let him have it.
Air Man: Leaf Shield (2 hits) Tip: Jump over and run under air shooters and get a clear shot. When he starts jumping, stand all the way to the left, because he'll stop right in front of you, and then turn around to shoot, making him a sitting duck.
Quick Man: Time Stopper (Full meter knocks off half of Quick man's energy) Tip: Run and shoot. Keep running and jump over the boomerangs when they converge and spread. He's weak, so pummel him.
Heat Man: Bubble Lead (4 hits) Tip: Shoot as soon as possible, and then jump over his Atomic Fire. Repeat. watch out, Crash bombs RESTORE his energy.
Wood Man: Atomic Fire (1 fully charged hit) Tip: Jump forward over his shields and fire rapidly! crash bombs can go through his shield.
Metal Man: Quick Boomerangs (4 hits) Tip: Run at him so he jumps over and launches 1 metal blade. Jump in between the Metal Blade and fire at metal Man. Repeat. And remember, other than that, he fires only when you do.
Flash Man: Crash Bombs (2 explosions) Tip: Jump just as you hear the pling sound, and always stay above him. Never make contact, unless you want to sacrifice energy and lure him into a crash bomb "time bomb".
Crash man: Air Shooter (2 hits) Tip: Jump and shoot at point blank range for guaranteed shots. the safer way is too shoot, and when he jumps over and launches a crash bomb, run away from the bomb and shoot him in mid-air. Remember, only one crash bomb can be on the screen at a time.
Robot Dragon:
Use Quick Boomerang. Try to stay on the right-most blocks.
Detachable Walls:
Use Metal Blade. (Remember you can aim in any of eight directions!)
Guts Dozer:
Use Bubble Lead or Quick Boomerangs. You can safely stand on the front end.
Orb Room:
Use Crash Bombs. Be careful if you blow all the walls away you won't have enough Crash Bomb energy to take care of the orbs. You can only afford to take out the two walls that directly block the orbs (use the Items to reach the rest), and even then you must enter the room with the Crash Bomber fully charged. You can, however, take out some or all of the walls, kill yourself, then recharge the Crash Bomber and come back to take care of the orbs. (The orbs will come back the walls won't.) Also, if you're having a hard time dodging their shots, try hitting START rapidly right before they connect, and they'll go right through you!
Wily 1st time:
Use Metal Blade or your arm cannon.
Wily 2nd time:
Use Bubble Lead. Whatever you do, don't make contact with the alien doing so will hack off about half of your energy. Notice the pattern in which the creature moves (it's the same pattern that its holographic projector makes after you defeat it, of course, since the alien was just a hologram). It's moving in a figure 8. Keep this in mind and you should escape with hardly a scratch.
Wood Man is invincible when using his Leaf Shield, except to the Crash Bomb. If the bomb misses a leaf, it will pass through and hit once. If it hits a leaf, it will explode and the explosions will hit multiple times.
On a similar note, try luring Flash Man into a corner and latch a Crash Bomb on the wall. As it explodes, it can hit him about 3 times if he stays in place.