Mega Man Zero 3 walkthrough

Story
The events of Mega Man Zero 3 take place two months after Elpizo's defeat in Mega Man Zero 2. Ciel has completed her research and has developed a new energy system for Neo Arcadia called the "Ciel System". When a crashed spaceship emits energy similar to the Dark Elf, Zero, Ciel, and members of the Resistance head out to investigate.

Main Characters

 * Zero: A Reploid that had been in hibernation in a lab for well over a century. He was discovered and reawakened by Ciel, a human scientist, to help save the world from Neo Arcadia.


 * Ciel: A human scientist and leader of the Resistance Base, a refuge for Reploids suspected of being Mavericks. She has developed an energy system that will most likely solve Neo Arcadia's energy crisis.


 * Dr. Weil: An evil scientist banished from Neo Arcadia a century ago for instigating the Elf Wars. He is the one responsible for corrupting the Mother Elf, which was meant to save the world.


 * Omega: A Reploid which was called forth by Dr. Weil. He played a major role in the Elf Wars, which killed more than half of the Reploids and humans on Earth. However, he has a secret...


 * Copy X: Appearing in the first Mega Man Zero game as the main antagonist, he was ruler of Neo Arcadia, before being destroyed by Zero. He has been revived by Dr. Weil.


 * Dark Elf: Originally called the "Mother Elf", she was a Cyber-elf created to end the Maverick Wars, but became corrupted in the hands of Dr. Weil.


 * Crea and Prea: Two baby elves that are in search of their mother, the Dark Elf.


 * Harpuia, Fefnir, and Leviathan: The three Guardians (the fourth had perished previously) of Master X in Mega Man Zero, are now working together with Zero.


 * The Eight Gentle Judges: Eight judges from Neo Arcadia that decided along with X (and later Copy X) if a Reploid called into question was a Maverick. They were brainwashed and modified by Dr. Weil to serve his purposes, and became Weil's Numbers.

Changes from the previous game

 * Weapons do not need leveling up.


 * Cyberspace can be accessed via holographic doors in stages. In Cyberspace, the stage becomes easier, not as much enemies, all enemies drop health bars, and certain Cyber-elves (Fusion and Satellite) auto-activate without dying or point deduction. However, going into Cyberspace decreases the mission score, making it harder to get an A or S rank.


 * Satellite elves are elves that are grown by being fed E-Crystals. They can be equipped (up to two at a time) to constantly benefit Zero without dying or causing point deduction. Normal Cyber-elves that die when used are now called Fusion elves.


 * E-Crystals can be fed to elves at anytime.


 * Secret Disks are hidden throughout the stages and inside of enemies. Some contain enemy, boss, and character bios as well as certain Cyber-elves. However, if any disks are locked, they can be taken to Cerveau to unlock them.


 * Custom chips replace the Form System from Mega Man Zero 2. Players can customize Zero's fighting abilities by equipping him with Head, Body, and Foot chips. Chips can be obtained from Secret Disks and some bosses.
 * Chips marked with a (*) mean that the chip is in the form of a Secret Disk somewhere in the stage.

Weapons

 * Main article: Zero's weaponry

Buster Shot:
 * 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.

Z-Saber:
 * A close range weapon that has wide coverage. Each Slash has varying slash pattern, and speed for different situations, such as Standing, Dashing, Walking, etc.

Recoil Rod:
 * A tonfa-like weapon that can attack in eight directions.


 * By charging the Recoil Rod and aiming it downward, it can be used to bounce up to reach normally inaccessible areas.


 * Charging the Recoil Rod and aiming it at enemies or certain objects will cause them to be knocked back.

Shield Boomerang:
 * Holding up the Shield Boomerang can make Zero bounce back enemy bullets.


 * By charging up the Shield Boomerang, it can also slice up enemies in a boomerang-like fashion.

EX Skills

 * Main article: EX Skills

EX Skills are special moves introduced in Mega Man Zero 2. Whenever facing a certain boss with an A or S rank, their special moves can be learned if they are defeated. However, to learn even more EX Skills, players must keep their A or S rank or have the use of a certain Cyber-elf (others will deduct points) to change their rank to an A. Some are executed through a certain weapon and some can perform better with a certain element; i.e, the EX Skill SplitHeavens (learned by defeating Hanumachine R) can be performed without an element, but in combination with the Fire Chip, allows Zero to gain more height on the attack.

Tips

 * A boss with no element has no weakness. However, Thunder beats Fire, Fire beats Ice, and Ice beats Thunder.

Intro Mission: Derelict Spacecraft
Make your way through the Grand Cannons and Shrimpolins with the Buster Shot and Z-Saber until Zero reaches a large corridor. After a cutscene with Harpuia, continue on destroying the Batrings, Shotcounters, Pantheon Hunters, and ice blocks as you go. Keep continuing up until you reach the boss door. After a cutscene with Leviathan and Fefnir, you will fight your first boss in the game.

Boss: Omega Reward(s): None
 * Health: 3 bars
 * Element: None
 * Weakness: None
 * Attacks:
 * Shoots energy rings in a set pattern. Avoid by moving, dashing, or jumping.
 * Shoots lasers that bounce off the ground.
 * His sword hovers above Zero, crashing down on him. Omega does this three times in succession.

After the cutscene between Dr. Weil and Copy X, you're back at the Resistance Base. After a short cutscene, you can save your data if you want. Go and see Cerveau (right exit of the commander's room, first door on your left). He's finished his Disk Analyzer, fixed Zero's Shield Boomerang, and created a new weapon, the Recoil Rod.

Obtain these items and head back into the commander's room. There you will be able to choose from four different missions.

Aegis Volcano Base: Neo Arcadia Army Recon
Watch out for the Heavy Cannons and also keep a close eye on the background. If the volcano erupts, watch out for falling rocks that appear on screen. Also be careful of the Volcaires that pop out of the lava. If you see an ocean of lava and platforms, watch your step. If your platform starts to rumble, the platform will start to rise, but be careful of certain ones; they rise up to a spiked ceiling that can can kill Zero instantly. Keep defeating the enemies as you go and stop when you see another ocean of lava. To get through this part of the stage, you must act fast; the platforms only have a limited amount of time before they sink into the lava. Go through the door and face another bunch of enemies and through the corridor you will face the mid-boss.

Mid-boss: Crossbyne

In this battle, you will face wave after wave of Crossbynes for 30 seconds. The Crossbynes attack by shooting needles in an "x" or a "+" shaped formation. There are two ways to win: Either defeat all the Crossbynes or survive for 30 seconds. However, it is recommended to defeat the Crossbynes if you're low on health or would like to refill your Sub Tank.

Keep going up, watching out for the Top Gabyoalls, because if Zero is on the same level of ground as they are, they will start spinning very fast. Also be careful of Lamplorts; they can be defeated by charging up the Recoil Rod to make them turn around so you can start slashing away. Another ocean of lava blocks your path. However this is more difficult than the last one. The same platforms that will sink will also be moving. Don't take a long time on the platforms as you might miss the next one. Be prepared to face the boss ahead.

Boss: Blazin' Flizard
 * Health: 2 bars
 * Element: Fire
 * Weakness: Thunder
 * Attacks:
 * Flizard attacks with his flamethrower.
 * Flizard fires three small spheres that set the floor on fire.
 * Flizard throws his frilled "collar" as a boomerang.
 * EX Skill - Fear Sprinkler: If the player is at an S or A rank, Blazin' Flizard jumps to the center of the room and fires a spray of fireblasts with his spinning frill in a set pattern.


 * Tip: By destroying Blazin' Flizard's tail, you will temporarily disable his bomb attack.

Reward(s): Fire Body Chip

EX Skill Obtained: BurstShot- By shooting a charged Buster Shot equipped with the Fire Chip, the bullet will explode on contact.

Oceanic Highway Ruins: Track Dark Elf Signal
Travel to the right until you see Childre Inarabitta standing around. He informs Zero about the Dark Elf being seen around the area and challenges him to see who will find it first. As Inarabitta hops into an impenetrable fish submarine, the challenge is not finding the Dark Elf first, but something a little more extra. Yes, you must get past the vehicle, but not to outrun it. Around the stage are switches Zero can step on to lower the water level, and by doing so, makes the upcoming boss battle a whole lot easier. However, the reason why you must get to the switches before the vehicle is because as the vehicle passes over a switch, a shockwave will destroy it and it cannot be activated. However, letting the vehicle go first will also destroy obstacles such as spikes and some platforms, making the entire stage easier to get through. As you continue left, step on as many switches as you can, and falter when encountering an obstacle such as spikes so the vehicle will pulverize it. Through the door will be this stage's mid-boss.

The Dark Elf has been spotted, along with two Pantheon Aquas. As one of them tries to attack the Dark Elf, the other becomes infused with Dark Elf power, destroying his partner.

Mid-boss: Modified Pantheon Aqua

The Pantheon Aqua has taken a form similar to Elpizo's second form from Mega Man Zero 2. This battle can be pretty tough, as its attacks include a laser being shot from one side of the field to the other, five arrows fired in five directions, creating falling debris, and grabbing Zero to drain his health.

Defeat this mid-boss and continue to look for more switches. Remember to stay back if there is an obstacle. Continue right to reach the door of the boss.

Boss: Childre Inarabitta
 * Health: 2 bars
 * Element: Ice
 * Weakness: Fire
 * Attacks:
 * Shoots missiles as high as the water level is.
 * Runs up the wall, planting mines as high as the water level is.
 * Drops down on the center of the field, sending out ice shards.
 * Ear Shot: A weaker version of his EX Skill, if the player is B rank or lower, Inarabitta will throw small ice blades from his ears.
 * EX Skill - Super Ear Shot: If the player is at an S or A rank, Inarabitta launches a giant blade of glowing energy at Zero from his ears.

Reward(s): Ice Body Chip, *Splash Jump Foot Chip

EX Skill Obtained: ThrowBlade- Fires a small shockwave from the Z-Saber. Used with the Ice Chip, the shockwave is bigger.

Weapons Repair Factory: Destroy Factory

 * Tip: If you have the Light Body Chip (defeat Deathtanz Mantisk), Zero can walk over the piles of rubble and it won't suck him in.

Watch out for the Eye Cannons as you progress. Getting caught by their surveillance camera automatically makes them shoot, so be careful. Also, little cracks in the wall contain Lemmingles that will pop out if Zero gets too close. As you go up, avoid getting hit by the hammers. Watch out for Snakecords, as you must defeat every segment to destroy them. Avoid the hammer and go down to face the mid-boss.

Mid-boss: Bee Server and Mellnets

This is a fairly easy fight. The Bee Server releases two Mellnets that home in on Zero, and shoots honey to slow him down. The Bee Server always opens its hive every time it does an attack, so keep attacking when that happens.

Keep dashing on the conveyor belts to advance. Watch out for the junk that comes and just use the Z-Saber to clear the way. There's more junk pits and some piles of junk that even have Lemmingles hiding in them. Destroy their homes and progress to the boss.

Boss: Hellbat Schilt / Devilbat Schilt (American version)
 * Health: 2 bars
 * Element: Thunder
 * Weakness: Ice
 * Attacks:
 * Shoots soundwaves that bounce off the walls.
 * Releases a swarm of bats from his cape.
 * Shoots electric orbs that return to him after a moderate distance.
 * EX Skill - Laser Creeper: If the player is at an S or A rank, Schilt hangs from the ceiling and warps around to one of three places at random, firing three electric beams from his ears that turn into three energy balls that crawl up the walls and across floor of the room.


 * Tip: Schilt will sometimes warp to avoid Zero while attacking. He will also recoil and take more damage than usual when attacked with a charged Ice Chip.

Reward(s): Thunder Body Chip

EX Skill Obtained: SaberSmash- Allows Zero to perform a downward thrust with the Z-Saber. If the Thunder Chip is equipped, it becomes an electric attack that creates two sparks when the blade strikes the ground.

Old Residential: Find Dark Elf

 * Tip: The Fire Chip will work great in this stage if Blazin' Flizard has been defeated previously. A charged Z-Saber slash will burn away the plants and vines to reveal new locations and Secret Disks.

Start the mission going to the right, defeating the Pantheons as you go. Watch out for Seimerans, these plant enemies that will reproduce if not destroyed. There are lots of doors in this stage also with Secret Disk, so keep your eyes peeled. Keep advancing up and go through the door. The two baby elves, Crea and Prea, are here looking for their "Mama". After a short cutscene, the two venture out of the room.

For the next part of the stage, you must be extra careful. Crumbling platforms will send Zero falling, and you'll never know when he will get crushed by spikes. Try to not get killed, and face the mid-boss.

Mid-boss: Megamilpa

This mid-boss, has only one, but deadly attack. Once it comes out of the ground, bullets will be shot from its segments. Megamilpa's only weak spot is the green orb on one of its segments. The boss will emerge from the ground in one of two patterns: It will travel straight up and then down, firing shots up and down the screen horizontally, or turn and curve into a half-circle, firing shots outward or inward. If Megamilpa emerges in the half-circle and bullets are being shot outward, move to the center of the screen allowing it to pass over, attacking its weak point in safety as it does so. However, if the bullets are being shot inside the circle, keep your Shield Boomerang up. Using the Shield Boomerang during this battle is advantageous; as standing to one side of the screen and keeping it up and charged will block Megamilpa's shots. When the green orb is in front of Zero, release the shield to attack. Also, if the Mailla Satellite-elf is equipped, Megamilpa's shots will be turned into vitality making its primary attack ineffective.

Continue up, but watch out for Pantheon Bombers in the stage. They will keep respawning, and throws bombs that explode in two directions. Grab a large energy pack just in case if your helth is low, and climb down. Watch out for Pillar Cannons on this part of the stage, as they can only be destroyed if their cannons are open. Jump across the pits and face the boss. Before you face the boss however, something catches your eye in the other room. One of Weil's Numbers found the elves, and you must fight the boss to get them back!

Boss: Deathtanz Mantisk Reward(s): Light Body Chip, *Auto-Charge Head Chip
 * Health: 2 bars
 * Element: None
 * Weakness: None
 * Attacks:
 * ​Shoots scythes that come back to him. He does this on the wall, or on the ground.
 * Shoots a scythe horizontally, but comes back vertically.
 * Thrusts his scythes if Zero gets too close.
 * EX Skill - Rock Breaker: If the player is at an S or A rank, Deathtanz will shoot lasers to the ceiling, causing a chunk of rock to fall down, and slice the pieces at Zero.

EX Skill Obtained: 1000 Slash- Repeatedly attacking with the Recoil Rod causes Zero to attack very fast with it.

After the fight, Crea and Prea go into a room with Dr. Weil. He says that he created the Dark Elf, their mother, so he is considered as their grandpa doing so. Before Zero can catch them, they teleport out of the room.

Complete all four missions to trigger a cutscene with Harpuia, Copy X, and Dr. Weil. Dr. Weil has prepared a missile that will strike Area Z-3079, a human residential area. The baby elves and Omega are also aboard the missile. Zero and Ciel are warned about the missile and Zero goes in an attempt to stop the missile.

Omega Missile
Start the mission going right. Watch out for Eye Cannons and Generator Cannons, as it sends out enemies that home in on you. Watch for Heavy Cannons also, as one portion of the stage shows a Heavy Cannon upside down. Keep dashing on the conveyor belts and make your way through the door. Climb up the ladders and get to the top platform. As you're on the platform, something unexpected happens...

The missile has been launched, and Zero hitches a ride on it to try and stop it.

This part of the mission starts by going left. Slice the Pantheons and PurpleNerples until you reach a part of the rocket splitting apart. Go inside the rocket and continue right, but you must act fast! Parts of the rocket will start splitting apart, and you must not get left behind! Whenever you see a rocket engine activating, jump on to the next part of the rocket. Get all the way to the end and face a surprising boss.

Boss: Crea/Prea Reward(s): None
 * Health: 3 bars (together)
 * Element: None
 * Weakness: None
 * Attacks:
 * ​Slams into each other, creating an explosion.
 * Fuses together to create one Cyber-elf, shooting lasers that split into two, crawling along the floor.
 * Crea can create a spinning ray, and Prea can sprinkle dust that slows Zero down.

The mission was a failure, and the missile had landed. When Zero regains conscience from the missile strike, the baby elves are reunited with their "mother". When Omega absorbs the Dark Elf, his armor becomes gold an purple in color, and becomes very powerful. When he is ordered by the baby elves to attack Zero, Harpuia comes just in time to stop him. But, Harpuia becomes severely damaged, and as Omega tries to attack Zero, Harpuia and Zero are quickly transferred to the Resistance Base.

Back at the base, Harpuia needs to rest up for a while for his wounds to heal. The Resistance Base gets a transmission from Copy X, asking for their surrender. He and Dr. Weil have organized a proposition: For the Ciel System, everyone's lives will be spared. But, seeing the damage done to the humans of Area Z-3079, Ciel refuses to give Neo Arcadia the Ciel System. When Ciel opposes, Copy X sends Neo Arcadian armies to attack the Resistance Base. Zero will intercept Neo Arcadian forces in the all-out invasion. With the task at hand, there are three new missions on the screen.

Twilight Desert: Engage Neo Arcadian Army
Tip: Using the Light Chip in this stage prevents Zero from getting sucked into the quicksand.

This mission is pretty straightforward. Slice up the Pantheons and watch out for Shrimpolins that pop out of the ground. Some of the terrain is this stage is not very hazardous; just jump when the quicksand sucks you in and the hills that drag you down do not really pose a threat unless if there are Floppers in the area. Make your way to the mid-boss.

Mid-boss: Or Wormer

The only hazard in this fight is the hill that drags you next to the boss. Even though the only attack it does is spitting out boulders, the PurpleNerples that pop out of nowhere tend to be also annoying. If their propeller gets slashed and they drop, jump over them to dodge. If you're attacking with the Z-Saber, never atack while on the ground, as the hill will drag you down and cause damage.

This part of the stage is also straightforward, with the same terrain as before. Check the pillars in this part of the stage to look for Secret Disks. Watch out for PurpleNerples that will swoop down on you. Also, a new hazard arrives on the stage. Occasionally there will be choppers that will keep sending out Pantheons and will fire rockets until you destroy the chopper itself. Destroy the choppers as fast as you can, but it's your choice if you wanna keep destroying them to rack up mission points in the enemy category. Slash the enemies that are in your way and get to the boss.

Returning Boss: Anubis Necromancess V

Tip: If you have played Megaman Zero and this is your first time playing this game, here are some of the changes made to this boss:
 * Anubis' element has been changed from Ice to Thunder.
 * Anubis has the ability to modify the stage's layout (quicksand, hills, etc.)

Reward(s): None
 * Health: 2 bars
 * Element: Thunder
 * Weakness: Ice
 * Attacks:
 * ​Throws his cane. It retuns to Anubis opposite from where he threw it.
 * Uses the two halves of his sarcophagus to smash Zero.
 * Creates Pantheon Zombies that pop out of the ground.
 * EX Skill - Dead Cane: If the player is at an S or A rank, Anubis will make his cane spin across the ground.

EX Skill Obtained: ShieldSweep- Makes the Shield Boomerang roll across the ground and return to Zero. In combination with the Thunder Chip, it creates electric sparks on the ground.

Forest of Anatre: Engage Neo Arcadian Army
Tip: The trees in the beginning of the stage can be burned with the Fire Chip.

This stage is very similar to the forest stages in Megaman Zero 2 (if you've played it). Like their stages, the trees can reveal things such as extra lives and Secs aret Disks. Slash away at the Mellnets, Seimerans and Generator Cannons as you go. However, burning away the trees reveal platforms that helps you avoid some enemies. Whichever one is fine; just get to the door.

Like Megaman Zero 2's stages, there's ruins in the forest. However, the ruins in the Forest of Anatre have switches not found in Megaman Zero 2. These switches open the walls in the ruins. You must be quick; getting smashed by one results in an instant kill. If you see boxes next to the switches, use the Recoil Rod to move it on the switch, keeping the wall open. Watch out for Tile Cannons, popping out on the ruins' walls. These enemies keep respawning every time you defeat it, and although it may be a nusiance to some people, they help to rack up mission points if you have not defeated that much enemies. Go through the door and face the boss.

Returning Boss: Hanumachine R

Tip: If you have played Megaman Zero and this is your first time playing this game, here are some of the changes made to this boss:
 * The only change in this is the room Zero is fighting in. Whenever Hanumachine R transforms into a fireball and bounces around the room, the blocks in the room can be broken, changing the stage's layout.

​Rewards: *Auto-Recover Head Chip
 * Health: 2 bars
 * Element: Fire
 * Weakness: Thunder
 * Attacks:
 * Transforms into a fireball, either ricocheting around the room or dashing from side to side.
 * Transforms into a fireball, shooting three fireballs.
 * Sends out monkey enemies that grab Zero and damage him.
 * EX Skill - Spinning Staff Monkey Dance: If the player is at an S or A rank, Hanumachine R sets both ends of his staff ablaze, and does an aerial spinning attack with it.

EX Skill Obtained: SplitHeavens- Performs a upward strike with the Z-Saber. With the Fire Chip, the attack gains more height than regular.

Frontline Ice Base: Engage Neo Arcadian Army
Starting at the entrance to the Ice Base, slash Pantheons as you go, underwater or not. Watch out for Sharkseal X's if taking the underwater route. There is another route that is above water, but either one is fine. Defeat the enemies and pass through the door.

At the next part of the stage, watch out for icicles on the ceiling and Heavy Cannons. The icicles can be cut with the Z-Saber, but move out of the way if an icicle shakes above you. Also watch out for Clavekers, little spider-like enemies that drop a barrage of bombs down on you. Advance through the door and face the boss.

Returning Boss: Blizzack Staggroff R

Tip: If you have played Megaman Zero and this your first time playing this game, here are some of the changes made to this boss:
 * After he jumps, standing near the ice clouds can freeze you.
 * His ice beam attack freezes the wall.

Tip: Attacking Blizzack with the Fire Chip will break his horns, disabling his icicle attack.
 * Health: 2 bars
 * Element: Ice
 * Weakness: Fire
 * Attacks:
 * ​Blizzack will jump around the room, possibly firing snowballs.
 * Shoots icicles into the air.
 * Fires an ice beam that pushes Zero back. Getting caught by the snowflakes will slow Zero down.
 * EX Skill - Double Blizzard: If the player is at an S or A rank, during his ice beam attack, instead of shooting just snowflakes, he will sometimes shoot ice shards that damage Zero.

Reward(s): None

EX Skill Obtained: BlizzardArrow- Charging the Buster Shot using the Ice Chip, it gives Zero the ability to fire ice shards from the Buster Shot.

Area X-2: Infiltrate Neo Arcadia
Slash at the Pantheons as you start right, but be careful of the Eye Cannons. Copy X constructed this stage to be Zero-proof, as this is one of the hardest stages in the game. As you defeat the first set of enemies, you will realize why this is one of the hardest. Most of this stage is covered by spikes! Floors, walls, ceilings, most of this stage is spikes! This stage can instant kill Zero quickly if you're not careful. The platforms that get though the spikes can also instant kill Zero, as he can get crushed when it hits the floor or ceiling. Just try and do your best to navigate through the platforms. Whenever the platforms rise up to the spikes, wall slide on the platform's side to avoid instant kill. After this point, Copy X has installed lasers that shuts off every now and then, but getting caught by one releases Gallisnis that zigzag up and down the screen. Make your way to the door and the next part of the stage.

This stage strikes a resemblance to the Neo Arcadian Tower in Megaman Zero. This part of the stage full of spikes and platforms attempting to smash you. Make your way though these, but watch out for Capsule Cannons on the walls. Floppers and Clavekers also inhabit this place, so watch out for the too. Do your best and make it to the boss.

Boss: Copy X Mark II

Tip: If you have played Megaman Zero and this your first time playing this game, here are some of the changes made to this boss:
 * Copy X's recovery attack can be used on lower ranks.
 * Copy X has a new EX Skill. Refer to the attacks section under Copy X Mark II.

Tip: Because of Copy X's extreme versatility with the elements and the ability to charge attacks, here's how his attacks will be grouped: Tip: Attacking Copy X with a charged Z-Saber will cause him to flinch, stopping his charge.
 * Health: 3 bars
 * Element: None
 * Weakness: None
 * Elements to attack with:
 * ​N= Normal
 * T= Thunder
 * F= Fire
 * I= Ice
 * C= Charged (used with any of the elements)
 * Attacks:
 * ​Performs a slide kick across the floor.
 * Does an aerial punch that homes in on you.
 * N: Shoots three shots (aerial and ground).
 * NC: Shoots one, powerful shot (ground only).
 * T: Shoots one to few electric orbs (aerial and ground).
 * TC: Fires electric sparks that bounce along the ground (ground only).
 * F: Shoots one to few streams of fire that travel in a curved path (aerial and ground).
 * FC: Shoots eight fireballs into the air (ground only).
 * I: Shoots ice that splits into smaller ice shards when it collides (aerial and ground).
 * IC: Shoots a vortex of ice across the field (ground only).
 * Recovers one health bar (used whenever he is 1 bar of health or under).
 * EX Skill - Reflect Laser: If the player is at an S or A rank, Copy X shoots a laser that bounces off the floor, walls, and ceiling.

Copy X is defeated again, and the real X appears. He tells Copy X that Weil was only using him as a tool for his own plans, but, out of frustration saying every treats him like a fool, he transforms into his final form. However, due to a bomb Weil planted on Copy X that would detonate when accessing his final form, Copy X explodes, and dies for good.

Reward(s): Quick Foot Chip

EX Skill Obtained: ReflectLaser- When the Buster Shot is charged normally, Zero can shoot a laser that bounces off the floor, walls, and ceiling.

With Copy X dead, the real X knew this plan was only a cover for his true ambition: For X to die, so Weil will become the new leader of Neo Arcadia. Dr. Weil also informs that if him and Neo Arcadia work together, they can put a stop to the Resistance, which he calls "extremists".

Back at the Resistance Base, Weil's plans are falling into place. However, if Ciel can gather information, he can tell where Weil's present location is. That doing so, there are four new missions to choose from:

Energy Facility: Search Facility
Watch out for Top Gabyoballs patrolling the area. Once you climb down, the room will darken, and this where the Thunder Chip comes in handy. Any short, orange poles in the stage can be attacked with a charged Z-Saber attack, which will light the room and repel the Mothjiros flying around. Watch out for the Capsule Cannons and Petatrias as you climb the ladders. Once you get through the door, there are buttons that spin round and round and Zero can get damaged if he touches them. The only way to make it out is to push in all of the buttons, and the Recoil Rod will be your helpful little tool here. A charged Recoil Rod attack to the buttons will push them in on one hit, making this room a piece of cake. Push in all of the buttons to make them stop rotating, and go through that door. Make your way through another batch of enemies and get to the mid-boss.

Mid-boss: Locomo IF

This battle can be somewhat tricky. the boss is stationed in the middle of the room, with platforms rotating around it. You don't have to stand on the platfoms, but you are in danger of getting damaged by the Top Gabyoballs on the walls and floor. This boss has two different attacks. When it is blue, it shoots ice-cold air upwards that can freeze Zero and when it is red, it shoots streams of fire downwards that can damage Zero from the eye, it's weak point. Even though this boss incorparates two different elements, it does not have a weakness.

Upon entering the next part of the stage, watch out for the Snakecords and the Floppers in this stage, too. In this part of the stage, there are cranes holding metal girders that you use as platforms to make it though the stage. There are also levers that are able to change the path of the girders. As you cross a spike pit traveling right, you must stand on the very edge of the girder to avoid getting killed by the spike ceiling, and also watch out for those Floppers. After slashing through Lamplorts, you will find yourself in another button room. The difference from the other room is that the buttons are raised slightly higher, and Crossbynes constanly appear in this room unless you push in all of the buttons. When you make it out, defeat another swarm of enemies and you will find yourself with more girders to navigate. There is also a lever here to switch the path which can also lead you to a Secret Disk. Watch out for Floppers and avoid the spike wall while navigating to get to the boss. Once you meet the boss, it turns out that the factory makes Dark Elf copies, or baby elves, and the factory became off limits so no one would get curious about it.

Boss: Cubit Foxtar Reward(s): Double Jump Foot Chip, *Frog Foot Chip
 * Health: 2 bars
 * Element: Fire
 * Weakness: Thunder
 * Attacks:
 * ​Cubit will jump and perform a backflip.
 * Fireballs surround her, and she throws them at Zero. They can be deflected with the Z-Saber.
 * Tranforms into five fireballs that dance around the room.
 * EX Skill - Fire Rain: If the player is at an S or A rank, Cubit stands in the middle of the room, shooting two sets of fireballs in a set pattern.

EX Skill: SoulLauncher- Aiming a charged Recoil Rod upwards will shoot up bullets.

Snowy Plains: Retrieve Data
This stage can be a rush if you take advantage of the technology in the stage. Watch out for the Shrimpolins that pop out beneath the snow. If taking the long way, watch out for the Gyro Cannons and Shellcrawlers. The Pantheon Bases in this stage ride on some kind of weird hovercraft thing, and if you destroy the rider, you can use them as transportation throughout the stage, but not for long.Before the mid-boss, there is a crumbling snow platform at the bottom of the upper platforms which you can use to get a Secret Disk. Use the hovercrafts to the best of your ability and get to the mid-boss.

Mid-boss: Blanc Wormer

The stage and the mid-boss resembles the mid-boss fight in Anubis Necromancess V's stage. Amazingly, this boss has a weakness, which is Fire, so you can beat it quickly. This mid-boss emerges from the bottom of the hill or the top of the hill, occasionally doing one of two attacks. He fires snow into the air to damage Zero, and snowballs that accumulate and get larger rolling down the hill. Both can be destroyed with the Z-Saber, and he's not really a challenge much, so this should be easy even for the beginners.

Watch out for the pits in this part of the stage. No one would rather care though, as the Pantheon Base enemy's hovercraft serves as tranportation here also. But if not taking the hovercraft, you should avoid the bottomless pits in the stage. Watch out for Mellnets and Generator Cannons and advance to the boss.

Boss: Glacier Le Cactank Tip: Watch out for the icicles on the ceiling while fighting this boss.
 * Health: 2 bars
 * Element: Ice
 * Weakness: Fire
 * Attacks:
 * ​Glacier will cling to the wall, swinging his arms and throwing ice shards.
 * Stretches out his arm which comes back to him slowly.
 * Jumps and shakes the floor, causing the icicles on the ceiling to fall early.
 * EX Skill - Ice Carnival: If the player is at an S or A rank, Glacier will swing his arm in circles, firing ice shards everywhere.

Reward(s): Spike Foot Chip

EX Skill Obtained: OrbitShield- Makes the Shield Boomerang revolve around Zero when charged. Using the Ice Chip, it revolves around Zero slightly longer.

Sunken Library: Retrieve Data File
In this stage, I would think twice before jumping into the water. This stage has a very dangerous hazard: When the water rises up into the highest point, it becomes electrified, and staying in there will take a chunk of health off. The Turtloid X's are enemies, but they can also be of your assistance if you know how tho use them right. They float among the electric, watery surface, and if you attack the arm thingy, it will turn over, becoming a platform to traverse over the electric water. Use them as best as you can, and get to high ground and to the door quickly.

Next, you will find yourself in the Data Room. There are files for Dr. Weil, Omega, the Dark Elf, and the Elf Wars located in a room past the Data Room. The room beyond is a grid of doors, in which some of them contain these files. Go to the monitor in the Data Room and search up one of the files. After that, the location of that certain file will be be shown, and you must go into the other room to retrieve them. The doors with the contained files have a purple hallway upon entering, so that is a clue to where they are. Collect all four files and face the boss in the room where you found the last one. Each room with the files has a different layout, so choose which file you want to collect last before fighting the boss.

Files:

File #650326- Dr. Weil:

From Neo Arcadia, creator of Omega, altered the Mother Elf, sparking the Elf Wars, banished from Neo Arcadia after the Elf Wars.

Room layout: Normal, rectangular room

File #815156- Omega:

The ultimate Reploid, created by Dr. Weil, possesses incredidible power when combined with the Dark Elf, banished to outer space to avoid another Elf War.

Room layout: Dr. Weil's room, but with spikes on the ceiling

File #351848- Dark Elf:

Officially known as the "Mother Elf." Creator unknown. This Cyber-elf was originally created for the purpose of restoring Maverick Programs to their original state, but the Mother Elf was altered by Dr. Weil so she could be used to manipulate Reploids, by freely rewriting programs.

Room layout: Right side of the room has a raised platform

File #945388- Elf Wars:

.........end of the.........Wars......Cyber-elves......used...........from this.............................................Elf Wars........................the us........................."Dark Elf," and copies.....................................amplify the power..............while........................at will.............the worst....in...................................................the war.....end...............Approximately 90%.................................................wiped..... (corrupted)

Room layout: Middle of the room has a small lower platform

Boss: Volteel Biblio Reward(s): Shadow Dash Foot Chip
 * Health: 2 bars
 * Element: Thunder
 * Weakness: Ice
 * Attacks:
 * ​Volteel will disappear, pop his head into one of the holes, and fire electric orbs that home in on you from his tail in another hole.
 * Electrifies the entire perimeter of the room.
 * Volteel lashes out his two tails at you.
 * EX Skill - V-Laser: If the player is at an S or A rank, Volteel shoots a laser in a sideways "V" formation.

EX Skill Obtained: V-Shot- Zero shoots bullets from the Buster Shot in a sideways "V" formation.

Giant Elevator: Search Facility
There are a lot of high places in this stage, so the Double Jump Foot Chip is recommended. The high places in this stage has Secret Disks and extra lives, and it most of the stage. An alternative would be to bounce up with the Recoil Rod, but it's not that good as the double jump. After progressing through the ladders and destroying the swarm of enemies, make your way down, but watch out for the Floppers. After you go through the door, you will land in an elevator. The only way for the elevator to reach its destination is to defeat every enemy, which consists of Clavekers, Shotloids, and the mid-boss. Because the Clavekers are shielded, a good way to defeat them is to knock them off the edge of the elevator, which destroys them. As for the Shotloids, act as usual and slash them to bits.

Mid-boss: Spearook

Just because you defeated all of the enemies, there are more, even after you defeat this guy. Spearook takes a similar form of Metarook from Megaman Zero. This one is actually faster, and this battle is more intense because of Zero in danger of being knocked off the elevator. This mid-boss attacks by thrusting itself at Zero with its spears or firing boomerangs. The weak spot is guarded by its body, but it can be revealed. Constantly slashing it will tip over the upper part of the body, making it vulnerable to slash. A good strategy is to fire an ice projectile, such as a charged Buster Shot using the Ice Chip, freezing it and tipping it over so the weak spot is open to attacks.

Finish off the next set of enemies to reach your destination. Continue down, out for the Floppers, and face this mission's boss through the door.

Boss: Tretista Kelverian Reward(s): Absorber Body Chip
 * Health: 3 bars
 * Element: None
 * Weakness: None
 * Attacks:
 * ​Detaches the dogs form his shoulders, which pounce around the room.
 * Grabs a box, throws it, and charges at it.
 * Shoots purple energy that travel along the ground.
 * Grabs a metal bar, bends it, and throws it like a boomerang.
 * EX Skill - Laser Claw: Tretista charges at the box, in which he occasionally shoots a purple laser generated from his claw.

EX Skill Obtained: GaleAttack- Zero can perform a thrust attack with the Z-Saber while dashing.

Complete the four missions and save your data (or not). Ciel has informed you that Harpuia's condition has improved, so it's best if you visit him. Harpuia wants revenge on Dr. Weil for stripping him of his position in Neo Arcadia. Though his wounds are not fully healed, Harpuia leaves the room. Head back to the commander's room. Ciel still has no information on Weil's location, but they might figure out what he is planning. Before talking about Weil, Ciel opens the Elf Wars file that's been fixed due to to corruption. It reads:

File# 945388- Elf Wars:

Near the end of the Maverick Wars, many Cyber-elves were used. The period from this time until the end of the fighting was referred to as the Elf Wars, as a result. In particular, the use of the gigantic elf known as the "Dark Elf," and copies of this elf, known as "Baby Elves," to amplify the power of Reploids, while controlling said Reploids at will, made this the worst war in recorded history. While use of the Dark Elf brought the war to an end in four years, approximately 90% of all Reploids, and 60% of all humans, were wiped out.

Ciel thinks that Dr. Weil might be trying to replicate these events. As Dr. Weil's voice appears on the monitor, it becomes clear that by using Omega, he has the power to control every Reploid on the planet. Because of this, Zero and Ciel are surrounded by resistance soldiers. With nowhere to run, X appears and knocks the soldiers unconsious by disabling the power of the Dark Elf. X informs Zero about Weil's location, in Neo Arcadia's underground power system, Sub Arcadia, where Omega is transmitting the power of the Dark Elf to all of the Reploids. With the coordinates of Sub Arcadia inserted, Zero steps in to stop Weil's evil plan.

Sub Arcadia
Make your way through the first set of enemies. As you drop down, enter Cyberspace for an optional boss. The rest of the stage will be summarized inside Cyberspace.

Cyberspace route:

As you make your way down the staircase, watch out for the spikes on the moving platform, and step through the door on your left. From there, use the teleporter and face a boss only found in Cyberspace. Yes folks, Phantom is back, and this battle with him is significantly harder than in Megaman Zero, as kunais will be flying literally everywhere!

Tip: If you are not inside Cyberspace, skip this section of the walkthrough.

Optional Boss: Hidden Phantom


 * Health: 3 bars


 * Element: None


 * Weakness: None


 * Attacks:

''Tip: The amount of kunais being fired in this battle makes it almost impossible to dodge them. Use the Shadow Dash Foot Chip, in which you can dash past them without it having to hurt.''
 * ​Hides among three clones while teleporting. The real Phantom has an irregular flashing pattern, while the rest are Pantheons in disguise. Strike a Pantheon, and Phantom will appear above Zero and stab his sword downwards. Too slow to react, and Phantom will quickly slash you while dashing.
 * Jumps and throws his shiruken, firing four kunais in "+" and "x" formations per revolution.
 * Throws his shiruken and rides it, quickly firing four kunais down on Zero before jumping off and stabbing down at Zero.

After the battle, Phantom encourages Zero to continue on and fight Omega. He then vanishes in a puff of smoke, never to be seen again. Grab the Secret Disk left behind by Phantom and exit the door.

Now, the stage continues here for the people not in Cyberspace. Navigate through the moving platforms, but watch out for the spikes. Advance through the door. Watch out for Pantheon Fists as you progress. Continue down, but watch out for the Cannon Hoppers as you go. Make you way through the corridor and drop down, defeating the enemies as you go. Make your way through the last enemies and face the boss. For those of you in Cyberspace, don't forget to exit out!

Boss: Crea and Prea (2nd and final encounter) Reward(s): Ultima Foot Chip (defeat Phantom)
 * Health: 3 bars (together)
 * Element: None
 * Weakness: None
 * Attacks:
 * ​Slams into each other, creating an explosion.
 * Fuses together to create one Cyber-elf, creating four rays and rotating across the field.
 * Moves out of the screen, and both travel the ground in a peculiar pattern.

Back at the Resistance Base, X has input new coordinates leading to Weil and Omega. The coordinates lead to an abandoned research lab next to where Zero had been hibernating. Prepare yourself; this is the last mission in the game. Let's stop Weil and Omega once and for all!

Final Mission
Start right and slash through the Pantheons. This next part of this stage bears resemblance to Area X-2's spikes, so watch out! Navigate through the platforms and go through the door.

And now it's time for a Megaman game tradition, yet again! Fight all the eight bosses (Weil's Numbers) all over again! Refer back to Aegis Volcano Base, Oceanic Highway Ruins, Weapons Repair Factory, and Old Residential on how to beat the first set of bosses. Here are the first set of bosses and their teleporter locations: Changes: The water in Childre's room is at full height.
 * Top-left teleporter: Deathtanz Mantisk
 * Top-right teleporter: Hellbat Schilt/Devilbat Schilt
 * Bottom-left teleporter: Childre Inarabitta
 * Bottom-right teleporter: Blazin' Flizard