

Entering the Cyberspace causes certain Cyber Elves to auto-activate without dying (both Fusion and Satellite that have an A-mark), even if not grown enough to be normally used, and these Elves do not affect the score. All enemies drop health items (instead of other items, such as ) in Cyberspace.

Mega Man Zero 3 can hold only one Battle Chip (all saved games use the same chip), holding the 'Z Saver' (a mistranslation of Z-Saber) in the beginning, and the virus enemies will not appear if the game contains the 'Z Saver' chip or no chips. Enemy appearances are less frequent and if a transfer of from a save has been performed, certain enemies from the series will appear.
