This can be changed right before the mission briefing. Stages that have a flashing border indicate a harder experience, whilst non-flashing ones will be easier. Depending on the weather, the terrain can be affected in a number of ways, such as removing, obscuring, or adding new obstacles. New to the series is a Weather System that affects the stages that Zero travels through. Though akin to a Satellite Elf, this one mimics abilities of other elves, allowing her to augment Zero's abilities of the Hacker, Nurse and Animal kind. In addition, the use of the Cyber-elf no longer penalizes the player for its usage, except for when Croire's total level is set above that of the current max level. The player may choose to talk to her for encouragement or hints at item recipes. This Cyber-elf can be upgraded by feeding her Energy Crystals. Depending on the name, her development will differ. as Zero uses just one, but very powerful, upgradable Cyber-elf named Croire (the default name is given by Alouette the player can choose another name by talking to Resistance members). The Cyber-elf system is simplified this time. In addition, when Zero defeats an enemy with the Zero Knuckle, he can steal that enemy's weapon and use it as his own, though he can also toss it away if the player wants to discard it or the weapon runs out of ammo.

This time, he starts out with the Z-Saber and Buster Shot again, along with a new weapon, the Zero Knuckle, a powerful weapon chip implanted in Zero's arm that allows him to punch enemies with incredible physical force. Zero does not gain any new main weapons during the course of the game. In turn, when all pieces of the 'Junk Armor' are equipped and the Cyber-elf is deactivated, Zero's attack power will drastically increase in exchange for halving Zero's defense (simulating the Proto Form from previous games). If two to four parts are incorrectly mixed together, a Junk part is created, which has no apparent use other than to make the 'Junk Armor'. The Elemental Chips, a mainstay of the series and technically a part of this system, are omitted. Players can still mix and match different chips for Zero's body to modify and improve his abilities however, instead of obtaining completed chips from bosses, Zero must instead create chips using parts dropped by enemies. The customization system from Mega Man Zero 3 returns in a more complex, detailed form. The gameplay remains the same as that of its predecessors: Zero must navigate through difficult obstacles while fighting Mavericks.

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