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- Awakening: (目覚め) The story begins with a Maverick called Pierrot attacking the city, which is defeated by X and Zero. In the Maverick Hunter base, Sigma begins a rebellion against humans, convincing several Hunters that humans are inferior to them. They attack the city and some Reploids try to convince X to shoot a human, but instead he shot the Reploids and tries to protect the city, passing through a highway and confronting Vile.
- Friend: (旧友) After the highway incident, Zero asks X to investigate a series of earthquakes that are happening near the base of the Maverick Hunter's 13th Polar Region Unit in Alaska. Once there, he discovers Mavericks took over the base and are using it to cause the earthquakes, which can create an avalanche and destroy the nearby city. At first, X wonders if this is being done by his friend Marth, but inside the base he discovers Marth was frozen by the one responsible, Chill Penguin. X obtains the Foot Parts in the base.
- Dignity: (誇り) X fights against Chill Penguin and defeats him with the help of his friend Marth. Some hours after Chill Penguin's defeat, X goes to a city that had a sudden loss of energy and is being attacked by Mavericks. The power plant was taken over by the Mavericks, and X enters there to defeat them. Inside the power plant, a shadowy Reploid observes him.
- Potentiality: (潜在能力) X fights against Thunder Slimer, and after his defeat he fights against Spark Mandrill.
- Requiem: (鎮魂曲) Sting Chameleon took over a wildlife reserve and brainwashed the animals with machines, also equipping them with weapons and using them to attack the nearby cities. Zero prepares to burn the forest to avoid more problems, but X asks to give him a chance to help the animals, going after the one responsible for this. Zero says he has until sunset to do so, and X rushes into the forest to find a way to help them. Along the way, he fights against RT-55J and finds the Armor Part, which protects him from the trap set by Sting Chameleon. X manages to free the animals and fights against Chameleon.
- Samurai: (サムライ) X defeated Sting Chameleon, but his buster became unusable because of the damage it suffered in the battle. When he meets with Zero again, they where surrounded by several Mavericks, but Armored Armadillo order a Met to repair X's buster and dispenses the minions, saying he wants to fight against X one-on-one in a duel in a mine.
- Successor: (継承者) X and Armored Armadillo battle one-on-one. At the end of the battle, Armadillo gives some explanation to X, and gives his life to protect him from Vile.
- Inferno: (地獄) X goes to a robot factory and fights against Flame Mammoth.
- Hope: (希望) X fights against Storm Eagle with the help of Zero.
- Mermaid: (人魚) Sigma's army mounted a base in the ocean, and X is sent there to investigate. There he meets Marty, a mermaid Reploid that helps him. X fights against Launch Octopus.
- Babel: (バベルの塔) Zero found Sigma's base and went there, and X tries to find him to help. Suddenly, a giant tower appears from the ground of the city X was passing by, and it destroys a large area around it with energy, and is charging to cause more destruction. X climbs the tower to stop it and fights against Boomer Kuwanger before it can destroy what was left of the city. Having trouble in the battle, X uses the energy of the tower in his buster to fire a powerful shot, destroying Boomer Kuwanger, part of the tower and his own buster with one shot. After this, Sigma's flying fortress appear and challenges X to fight against him.
- Farewell: (さらば、友よ) In Sigma's fortress, X passes through several defeated Mavericks, and finds Zero aprisioned by Vile. X can't fight against him with his damaged buster, but Zero manages to break free and explodes on Vile, damaging him and his Ride Armor.
- Victory: (勝利) The final showdown between X and Sigma begins in Sigma's throne room. Though overwhelmed by Sigma's power, X managed to defeat his first form. As Sigma morphed into his gigantic final form, X had not enough energy to fight him again but instead, send Sigma's fortress crashing to the atmosphere by disrupting the controls aboard. The fortress including Sigma was destroyed during the atmospheric entry. X was protected by the protective coat left by Sigma and survived.
- Revival: (復活) Some time after Sigma's defeat, X decided to seal away his weapon and not using it anymore, because he did not want to be forced to kill anyone like the battles in the previous war. Various incidents erupted in the next six months and it was found that the culprit was the rebirthed Sigma. X had no choice but to remove his weapon's seal to fight Sigma once again.
- Wiseman: (賢者) Dr. Cain. Wire Sponge.
- Duel: (決闘) Flame Stag
- Glittering Death: (輝ける死) Crystal Snail
- Antlion: (蟻地獄) Overdrive Ostrich
- Illusion: (幻) Overdrive Ostrich part 2 and Chop Register
- Possibility: (可能性) Magna Centipede
- Pirates: (海賊) Bubble Crab
- Weakness: (心の弱さ) Morph Moth
- Healing: (いやし) Wheel Gator
- Hidden Weapon: (隠されし武器) X-Hunters (Serges, Agile, Violen)
- Inevitable Battle: (避けえぬ闘い) Black Zero
- Miracle: (奇跡) Sigma
- Malfunction: Mac and Maoh the Giant
- Snowman: Blizzard Buffalo
- Cocoon: X and Zero fights against Tunnel Rhino. After his defeat, Doppler creates a wire cocoon around Tunnel Rhino to act as shield, but they manage to defeat him.
- Strength: Zero fights against Blast Hornet.
- Conscience: Neon Tiger
- Peace: Dr. Cain analyzes Blizzard Buffalo, Tunnel Rhino, Blast Hornet and Neon Tiger to discover why they went out of control, and a worm-like machine jumps from them to other Reploids, including X, making them go out of control. The Maverick Hunter base is attacked by Bit and Byte, and Zero tries to stop them, later having the help of other Hunters. X recovers from the accident and helps them.
- Sniper: Crush Crawfish
- Big Bang: Volt Catfish
- Remain: Toxic Seahorse
- Vengeance: Gravity Beetle wants to avenge Boomer Kuwanger and attacks the city with a giant beetle-like machine.
- Funeral: Bit and Byte defeat X and Zero.
- Comrade: With X and Zero imprisoned, Bit makes an announcement in Doppler Town saying they will be killed by a drill, and a Maverick outbreak happens in the town. Marty appears in the Maverick Hunter's base and Cain asks her to take four chips to X, freeing him.
- Hatred: Doppler merges Bit and Byte into Godkarmachine O Inary.
- Wrath: Dr. Cain tries to repair Dr. Doppler, but Doppler decides to destroy himself.
- Oni: X fights against Vile in Sigma's fortress.
- Shine: X fights against Sigma in his most powerful body.
- Zero 1. Mars: Zero has a nightmare with Sigma. He meets the Repliforce.
- Zero 2. Ikaros: The Maverick Hunters and the Repliforce work together in one mission.
- Suspicion: (疑惑) Sky Lagoon is attacked by Mavericks, and it's believed Repliforce was behind it.
- Uprising: (蜂起) Repliforce announces their wish for independence.
- Jungle: (密林) Web Spider
- Ocean: (大海原) Jet Stingray
- Conviction: (信念) Split Mushroom
- Ice Fang: (氷の牙) Frost Walrus
- Strength: (力) Frost Walrus part 2
- Big Tree: () Zero fights against Colonel
- Diving: (潜行) Zero is in a virtual training program when something goes wrong. He see strange images of Reploids killed by him, Sigma screaming, and a mysterious scientist. He fights against Cyber Peacock.
- Running: (疾走) Slash Beast
- Fate: (運命) Zero fights against Colonel and Iris, and X against Storm Owl and Magma Dragoon.
- Tears: (涙) X fights against Double. General sacrifices himself to stop the weapon.
- Zero is often seen without his helmet in the manga. X is also shown to be able to remove his helmet, although he is always out of view when he does.
- The Rockman X4 manga did not receive a complete compilation publication due to complications with Bom Bom Comics, the second and final volume stopping halfway through the story. It was not until the 2005 re-releases from Fukkan that the X4 story was finally released in its entirety.