Even though Omega has been defeated and the world is safe from the Dark Elf, the human utopia known as Neo Arcadia has fallen under the rule of Dr. Weil, turning the once-peaceful city into a wasteland. At the start of the game, we find a moving trailer of humans fleeing from Neo Arcadia. With Weil's soldiers known as Variants chasing after them, Zero attempts to guide the trailer to safety.
Changes from the previous game
- All weapons are given to you from the start.
- To get chips, you must synthesize them from fallen enemy parts.
- There is only one Cyber-Elf in this game. However, it exhibits Nurse, Animal, and Hacker traits and must be fed with Energy Crystals to level up and learn more skills. For every level you use up, it becomes the Elf Level. Do not exceed the Max Level in a mission, or you'll lose points.
- All 8 main missions are availailable from the start.
- No elemental chips are available, instead using EX Skills as elemental attacks.
- The Weather System is introduced in the game. Weather icons appear on the mission screen, and in Normal Mode you are able to set the weather to your choosing. Weather icons with a non-flashing border indicates your mission will be easier to complete, but will result in a mission penalty. Weather icons with a flashing border indicate the mission will be harder to complete, but if you defeat the mission's boss, you will obtain an EX Skill regardless of rank (Normal Mode only).
- The game difficulties have been integrated as gameplay options.
- An "Easy Mode" has been added to the game, in Easy Mode, the Cyber-Elf you obtain is Lv. 5, and you can only use abilities Lv. 5 or under. Aside from that, death hazards are no longer instant death, all Mission Weather is set to "easy" (non-flashing border).
Main article: Zero's weaponry
- Zero's long-ranged weapon in the Mega Man Zero series. It fires energy bullets horizontally with narrow coverage, and can be charged to fire larger, more powerful shots.
- A close range weapon that has wide coverage. Each slash has a varying pattern, and speed for different situations, such as standing, dashing, walking, etc.
- A hand weapon with a grabbing attack.
- Use it on enemies to steal their weapons. The amount of times you can attack range from one to infinity. You can only carry one enemy weapon at a time.
- Yank out objects.
- A very useful tool in boss battles. For example, when Noble Mandrago's head pops out of the ground, you can yank her out using the Zero Knuckle.
Destroy the Variants as you start right. The road under you is dangerous, and if you touch it, you'll take big damage. You can steal the Variant's fire attack to burn away the exterior of some of the trains, revealing Energy Crystals and extra lives. A useful thing to do is Zero Knuckle the bomb crates, as they are helpful defeating the boss ahead. You can also yank the LamplortX's shields off, leaving them vulnerable to attack and give you cover from projectiles. Keep going right until you enter a cutscene. After the cutscene, continue right, watching out for the missiles and GyroCannonHs and face the boss.
Boss: SubDesert Core
- Health: 2 bars
- Element: None
- Weakness: None
- Shoots a blue laser across the field. Avoid by dashing under it.
- Shoots two purple lasers that travel across the field in a zigzag pattern.
- Summons BeamWalkers to attack Zero.
- Tip: By tearing out the wires under the core with the Zero Knuckle, you can shorten the width of the blue laser until it becomes permanently disabled.