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- Battle Pharaohman
After completing the game, go to the WWW area from the Undernet. Unlock the security cubes with a S license lock and you will get to Pharaohman. This battle is similar to the fight with Thunderman. He has two coffins that will do most of the attacking for him, but he does not attack very often. When he does, he will put a switch on the battlefield that activates a trap. For this battle, chips like Stepsword and Cannonball work very well, but the coffins act like shields and can block chips such as Cannon very easily. Pharaohman has 1200 hp.
- Defeating Gateman
If you have the style Fireguts, charge your attack by holding A then release it. Even if he has used Remo Gate, the flames will pass right through, and if aimed correctly, will hit him regardless. The flames also destroy his soldiers easily.
- Defeating Gutsman
During your battle with him, move Mega Man to one of the front squares. When you do this, Gutsman will approach to punch you. Dodge the punch by moving sideways, then immediately move back to the original location and hit him with a chip. He will now move to a different square, then return to hit you again. When this happens, do the same thing again. When you run out of chips, charge your Megabuster and hit him with it. Note: This strategy will only work with a Guts-style Mega Man.
- Gamecube logo
After defeating Shadowman, reenter the main mother computer. Go to the back of the computer. Stand in front of the "mother computer main server", where Shadowman was standing before you fought him. Slowly go to Megaman's right. Upon a stack of cubes with purple, squiggly lines on them will be the Gamecube logo.
- Hard mode
Successfully complete the game with all five stars. Highlight the "New Game" option at the title screen, then press Left(2), Right, Left, Right, Left, Right(2). The ''New Game'' option will turn orange to confirm correct code entry. Select that option and the "Netbattle" option will not longer be available. Save the game, then restart. A "Hard Mode" option will now be unlocked under the ''New Game'' and ''Continue'' options.
- Shadow Wide Sword
If you have any type of Shadow Chip and already upgraded the charge in your Mega Man profile, equip the Shadow Chip during battle and charge your Blaster while you are in shadow mode. When the charge is ready, release A and you will immediately transport to the enemy panels. The closest enemy to you will be hit with the Shadow Wide Sword, as well as anyone else in a vertical angle. The damage is the same from your Blaster when charged.