The year is 22XX. Even after the [real] annihilation of the Next-Generation Reploids that could go MAW (Maverick At Will), the Sigma Virus still spreads across the galaxy, spread by the escapist Reploid, Spider. As these events go on, a new group of Reploids called the Calamity appears, bidding on taking over the chaotic galaxy with thier leader, Newclear Solarraven. X, Zero and Axl must rely on themselves to save the universe from these 'Mavericks'.
Mega Man X: Reincarnation of the previous Mega Man, his Variable Weapons System lets him obtain weapons from the enemies he defeats. He also wields the X-Buster, which can be charged or even charge up weapons for greater effect.
Primary Armor - Excalibur Armor - Takes the appearance of a medieval knight's armor.
Secondary Armor - Duo Armor - The remains of an old crusader robot.
Zero: Wily's finest, and most good-hearted, creation. He learns techniques by using the data from fallen Mavericks. His Z-Saber, however, is limited to close-range fighting.
Armor - Absolute Zero - Created from burning ice on certain planets into metallics.
Axl: The newest Maverick Hunter, originally a prototype for New Generation Reploids that were now banned. He can use a whole variety of different weapons, including double blasters, and utilizes the Copy Shot to transform into different enemies.
Armor - Tabby Armor - Appearance similar to Oddeye Bakeneko.
Sonikku Krakenite - Underwater Base: Sonikku Krakenite is a Reploid originally created to map the surface of underwater planetoids. Presumed lost in the ocean of a planet he was examining, he built an underwater base on that planet, building up a supply of bombs built to cause tsunamis from landslides. He is equipped with dual cannons that emit small, siezmic explosions that can also scan enemies.
Sniperscope Eagleloomer - Air Force SP: Known by his comrades as 'Hawkeye', his main ideals was patrolling large, airy planets where it was impossible to scan all the colonies at one time. He is slightly based on Storm Eagle in design, but was more lightweight and had better eyesight. His Air Force of mechaniloids, under his command, are blockading a patrollable planetoid. He specializes in long-ranged weaponry, such as sniper-type weapons, but may resort to short-ranged combat.
Guardian Wolverine - Prison Fortress: Guardian Wolverine was built specifically to guard galactic-scale prisons. He was retired from duty because of his practice of deleting any imprisoned reploids in a fight out in the commons area. Back on duty, he keeps control of a prison that holds many captured Maverick Hunters, which included Magmard Dragoon. He can use his sharp claws to block certain attacks.
Virtua Nonatail - Training Area: Virtua Nonatail was the basis for a Reploid much later built - Cubit Foxstar. But beyond that, Virtua is a master of deception above all and has an IQ of 300, even hiding her own gender from view, appearing male at first glance. She now 'trains' new Mechaniloids to hunt down humans. Her 'tails' can fire energy pulses to paralyze or burn foes, and she can teleport.
Cavedigger Cobraslither - Underground Workspace: Cavedigger Cobraslither was a mining Reploid working on rock-covered planetoids. He was retired because he hid all the treasures he found on the job there to keep and sell as his own. He now works to undermine potential Maverick Hunter bases. On his forehead is a powerful rocket-launcher able to tear apart solid steel.
Coldiced Pisceskiller - Frozen Wasteland: This ice-cold swordfish-type Reploid was built with armor made of frigid ice, making him less mobile but more resistant to attacks. If he were let out into an extremely warm area, his outside would literally melt to reveal the clockworks inside. He is extremely territorial, and will attack all that enter into his area. Just touching him can freeze Reploids solid.
Poisonous Flytrap - Vast Jungle Area: Being a plant-type Reploid, his main purpose was attract potentially dangerous wildlife to him, so they could be slain and/or entangled by his abilities. He now works to attract Reploids to him, so they could be slowly entangled to death. He is equipped with poisonous gases and can even heal his own injuries.
Energysucker Screechlots - Old Satellite: A bat-type Reploid, he is equipped with darkvision, and was assaigned to give power to old buildings. When he became Maverick, he reversed the effects to suck the power out of most Reploids. His bite can sap your energy bit by bit if you can't escape.
Seizmic Wave: X's weapon from Sonikku Krakenite. It is a powerful attack that, when equipped, it can scan an enemy's HP. Charge it, and a much larger blast is released in an area centered around X.
Landslide Trigger: Zero's technique from Sonikku Krakenite. This attack is an extremely powerful Giga Attack, which does Earth-type damage to anything in the vicinity.
Sounddrifter: Axl's gun-type that he can buy after beating Sonikku Krakenite. This weapon can reflect off walls and scan an enemy's HP when it is equipped. The weapon releases a blast after it hits an enemy.
Guided Buster: X's weapon from Sniperscope Eagleloomer. This attack releases a single bullet-like attack that goes forward a little bit, then homes in on the nearest enemy. When holding the Left Mouse Key, you can guide it to the mouse's position. Charging the weapon releases five homing shots at once.
Hieijin: A returning technique Zero learns from Sniperscope Eagleloomer. In midair, Zero releases a small energy dart that homes in on enemies. It can also be fired up and down, or it can be held onto for later.
Sniper Rifle: Axl's gun-type that he can buy after beating Sniperscope Eagleloomer. Using the Left Mouse Key as a guide Axl can basically snipe on any enemy onscreen, including himself.
Extend Shield: X's weapon from Guardian Wolverine. X enters a guard stance, shielding him from certain attacks. The guard can be broken by a heavy attack or a foe running into you. Release the weapon to counterattack. When charged and released, a howl is released that removes projectiles from the screen.
Gokumonken: A returning technique Zero learns from Guardian Wolverine. This weapon, however, immediately counters an enemy if one nears Zero and shields from all projectiles.
Tinatium Arm: Axl's weapon that he can buy after beating Guardian Wolverine. This weapon is a short-ranged melee attack, but it shields against projectiles if timed correctly.
Projection Strike: X's weapon from Virtua Nonatail. X creates a minor clone of himself a set distance away from him in any of the cardinal directions. This energy clone mimics all of X's actions except for attacks and also damages enemies it touches. The charged version lets X switch places with the clone, or as far as he can go without hitting a wall.
Sougenmu: A recurring technique Zero learns from Virtua Nonatail. Zero creates a copy of himself that not only mimics his movements but his attacks as well. The clone dissapears after some time.
Mirror Me: Axl's gun-type that he can buy after beating Virtua Nonatail. The weapon simply creates a clone of Axl to mirror his movements, giving him the benefits of Sougenmu.
Removal Bomb: X's weapon from Cavedigger Cobraslither. X fires out a bomb-like projectile that, if either set aflame or hitting a wall, explodes instantly, damaging anything in its radius. Charged, four bombs are fired at different arcs each.
Ganzanha: A returning technique Zero learns from Cavedigger Cobraslither. Zero, throwing the Z-Saber into the air, punches the ground with enough force to create a shockwave, breaking enemy's guards.
Napalm Packs: Axl's gun-type that he can buy after beating Cavedigger Cobraslither. Axl throws a sphere-like projectile in a medium arc, that will bounce along the ground a while before exploding even if an enemy touches it.
Ice Dasher: X's weapon he gains from Coldiced Pisceskiller. As X dashes, he rams into enemies with immense force and freezes then solid. This attack can douse fire or freeze water solid, giving you reach to new areas. Charged up, the dash will go farther and spread damaging icicles where you dashed, damaging enemies.
Hisouishou: A returning technique that Zero learns after beating Coldiced Pisceskiller. It performs an ice-elemental Air Dash and can be used similarly (Zero can double-jump instead of air-dashing like X.)
Glacier Shotgun: Axl's gun-type that he can buy after beating Coldiced Pisceskiller. The weapon releases multiple, small ice blasts in several directions, which freeze enemies. They vanish if they hit any hard surface. Deadly Shroud: X's weapon he obtains from Poisonous Flytrap. This weapon is a simple projectile that, while moving forward constantly, can be steered slightly by the up and down keys. Releasing it at any time releases a poisonous gas that paralyzes enemies.
Virus Break - Roboenza: Zero's technique he learns from Poisonous Flytrap. This weapon surrounds Zero with an ominous shroud that paralyzes enemies instantly when they enter the area.
Reploid Spray: Axl's gun-type that he can buy after beating Poisonous Flytrap. The weapon is short-ranged but instantly paralyzes enemies. If the enemy flies, it will fall down instantly like with the other weapons.
Vampire Strike: X's weapon that he obtains from Energysucker Screechlots. This weapon emits a blast of energy that drains the energy from enemies it hits. It reflects similarly to the classic-series Noise Crush weapon. When charged up, it deals more damage and thus sucks more HP, but becomes short-ranged.
Ratsetsusen: A returning technique Zero learns from Energysucker Screechlots. Zero spins in midair as to damage enemies, becoming invulnerable as he eliminates enemies.
Darkvision: Axl's gun-type that he can buy after beating Energysucker Screechlots. Less of a gun and more of a sight-type, it lets you see an enemy's HP. Equipping it as a secondary to the Sniper Rifle extends its vision range.
Excalibur Armor - This armor, used for X, is split into four parts and focuses on defense. It is rumored whoever wears this armor will protect allies at all costs.
- Excalibur Headpiece - Increases the recovery rate for X and the reserve partner.
- Excalibur Chestpiece - The damage dealt to you will give you 10 metals per damage taken.
- 'Excalibur Sword' - Unlocks a third charge shot which, while short-ranged, breaks enemy guards and deals more damage than a regular charge shot.
- Excalibur Boots - Lets you walk on spikes, but only for a certain time represented by a red bar above the character. This also benefits the other ally.
- Excalibur Chip - If he has all other pieces of the armor, X's sword can also be represented as a rising slash (akin to Ryuenjin) or a downward stab that can create a shockwave (Rakukoujin-style). After getting this chip, keep in mind it is permanately fused to X.
- Giga Attack - Excalibur Soul - Increases speed, jumping height and defense for allies in reserve until they are damaged by a heavy attack.
Duo Armor - This armor, used by X, is said to be the remains of a benelovent robot from the year 20XX. This armor is seemingly protected by a strong, blessed aura, and whoever wears this armor will either be cleansed of any ailment or immediately disposed.
- Duo Helm - Decreases the amount of Weapons Energy used per shot. X will also slowly recover energy for the currently equipped weapon while standing still.
- Duo Body - Decreases damage dealt to X by 33%. For enemies that only do 1 or 2 points of damage, X is nigh invulnerable.
- Duo Hand - Unlocks a third charge shot that deals minor damage, but if the enemy is defeated by this attack, you get metals equivalent to the enemy's max HP regardless of the item dropped.
- Duo Speed - Allows you to hover into the air before Air Dashing. You are also invulnerable while dashing.
- Duo Chip - If he has all other pieces of this armor, the recovery rate for allies will triple when standing still. After getting this chip, keep in mind it is permanately fused to X.
- Giga Attack - Benevolent Power - Does a Nova Strike straight downwards. If it hits solid ground, all enemies on screen will be turned into medals. This also removes 50% of a boss's HP and turns it into medals.
Absolute Zero - This armor is used by Zero, and can be found by collecting all the Rare Metals in each stage, including the penultimate stage.This armor boosts Zero's strength and lets him hover in the air, at the cost of a halved defense score.
Tabby Armor - The armor, built from the remains of Sigma's final body after it was cleansed, is obtained by beating the main game once. The armor itself is made of certain fur that deflect any and all non-Reploid projectile attacks. In addition, Axl can copy his foes indefinitely.
Ultimate Armor - This armor is the last prize in the game, gained after beating all the training sessions - as well as the game. This armor boosts strength, defense, speed, jumping height and firing rate and can be equipped to any character. However, Metals cannot be obtained with this armor.
Dynamo: Yep, our old mercenary friend Dynamo is back for a rematch. He joined Calamity because they bid the highest. Our friend has many moves obtained from the other mavericks in the game. Once you beat him, he goes out with a bang.
Newclear Solarraven: The 'leader' of Calamity. He is based off the yatagarasu, a three-legged crow said to sit on the sun (the 'third leg' is a cane-type structure.) He has a twin sister, specifically, another female Reploid built with similar DNA. He mostly has powers involving radioactivity and nuclear explosions.
Oddeye Bakeneko: Supposedly Newclear's right hand man. He has some secrets about him that he will never tell, and his name has never been recorded in any list of alive Reploids. He is quite an agile Reploid, using his claws to attack enemies.
Oddeye Bakeneko is actually Sigma's powerful disguise that he took to spread the Sigma Virus. He blackmailed Newclear Solarraven into creating Calamity, using his 'sister' as the blackmail.
The final encounter against Oddeye Bakeneko takes place on a satellite above a destroyed Earth. The backdrop is a japanese-style painting of a stormy seabed. Oddeye now comes equipped with twin metal swords, the Nekonusume's Secrets and attack with some of Zero's techniques.
Second Phase is Sigma himself. He joins the two blades together into a scythe, and they fuse with energy. Sigma still has paw-like hands even in this form, and uses different strategies depending on your player character.
Third Phase, Sigma (in virus form) fades away for a while before a new body resembling a large cat appears from stage center. This form, only damagable by a crystal on the forehead, can electrify parts of its fur and unleash smaller enemies, making the battle annoying to perfect. It doesn't help that you can only get a few shots in at once.
"I'll never die... no matter how many times you destroy my bodies, I'll always return..."
Sigma's final words, as his body floated onward to slowly decompose in the vastness of space. But for how long would this peace last, X wonders to himself...
X: "Sigma's right. It'll never end..."
Axl: "What? That's nothing I'd hear from X, universe's most powerful Maverick Hunter!"
Zero: "X's right, Axl. As long as the soul remains, there will still be some remainder of Mavericks to bring to justice."
Axl: "Cheer up, guys! At least peace reigns for now, right?"
Axl: "Right, guys?"
Zero: "We should return to base. Our mission is complete."
Axl: "Yeah... let's go..."
- Back at the Maverick Hunter base...
Alia: "Good work, you three. Thanks to you, the Maverick Virus is stopped for the time being."
Zero: "Huh. Hardly a fight. You said Sigma'd be powerful this time, Alia!"
Alia: "Strange. Zero, you're a bit cheery today."
Axl: "C'mon, Alia. Even reploids like Zero laugh once in a while."
Alia: "Say, since you're a bit restless, how about a little session in the holodeck?"
Axl: "What's it gonna be, Alia?"
Alia: "Kaiser Sigma data, level maximum."
Palette: "Did someone say Holodeck?"
Alia: "Do you wish to join too, Palette?"
Palette: "Sure! Beats sitting around and giving information all day!"
The three maverick hunters laugh, as the screen fades and the credits roll.
Overall, a happy and ominous ending all in one.
After beating the game, you also get the Tabby Armor for Axl.