Mega Man Zero (Nintendo Cinematic Universe)

Mega Man Zero is a Japanese graphic novel series.

Volume 1
100 years after the Maverick Wars, the Reploid Zero is awakened from a century of sleep to aid a human scientist named Ciel and her resistance force in a fight against the utopia of Neo Arcadia, which is attempting to unjustly wipe out all androids it views as threats.

Volume 2
Zero's battle with Neo Arcadia rages on.

Volume 3
The true culprit behind the Elf Wars is revealed.

Volume 1

 * Roughly 100 years following the end of the Maverick Wars, the heroic Maverick Hunters X and Zero have long since vanished.
 * A human scientist named Ciel, her Cyber-elf Passy, and other Reploid companions are being chased through an abandoned underground laboratory. Their relentless pursuers are mass-produced androids called Pantheons, among other terrible machines.
 * After taking heavy losses, Ciel, Passy and the remaining troops arrive at a sealed chamber containing Zero, who has been in stasis for a century.
 * Passy sacrifices itself to awaken Zero, who is amnesic.
 * Ciel, desperately seeking his help, explains they live in a world where Reploids are incorrectly accused of being Mavericks and systematically "retired", apparently under the direction of the once-famed Mega Man X. Shocked at this revelation and filled with doubt about his own identity as the Maverick Hunter of legend, Zero helps Ciel escape and joins her Resistance to fight against X and the utopia known as Neo Arcadia.
 * Zero conducts missions on behalf of the Resistance in order to buy Ciel time to create a new energy source that will provide everyone with a safe place to live.
 * One day, the base is attacked by Neo Arcadia, forcing everyone to flee.
 * In the midst of the chaos, Ciel confesses to Zero that she helped create Neo Arcadia as a utopia where humans and Reploids were finally able to live in peace with X as their leader, but her plans fell apart when an energy shortage crisis began and X mysteriously disappeared. To counter this, while at age six, she created a "copy" of X to be its new leader.
 * Copy X strived for X's ultimate desire for a peaceful world, but lacked the original's moral judgement.
 * Believing that the Reploid race posed a danger to humans, Copy X began an operation to brand any Reploid whom he believed to be a menace to humanity as a Maverick and annihilate them without a fair trial, in order to reduce energy consumption.
 * Zero invades Neo Arcadia and battles his way through the Four Guardians: Sage Harpuia, Hidden Phantom, Fighting Fefnir and Fairy Leviathan.
 * Phantom self-destructs in a last ditch effort to destroy Zero, but fails, while the other three manage to escape.
 * Copy X is eventually defeated, who also self-destructs in an attempt to take Zero with him.
 * Zero escapes just in time from Neo Arcadia as Copy X, and everything around him, is destroyed.
 * Running low on energy, Zero collapses in a nearby desert.
 * A faint figure appears and reveals itself as the real X, now a Cyber-elf, who has been Zero's guide the entire time. X explains that he grew tired of fighting and, without a physical body, has left Zero the responsibility of bringing peace to the world. As X vanishes, Zero finds himself surrounded by an army of Pantheons.
 * Zero accepts X's words and promises to continue the fight against Neo Arcadia.
 * The final scene shows Zero as he dashes into battle against the Pantheons and slices one in half.

Volume 2

 * One year has passed since Zero defeated Copy X. He has since separated from Ciel and the Resistance, now wandering the desert and defeating countless Pantheons.
 * The three surviving members of the Four Guardians have assumed command of Neo Arcadia, with Harpuia as the leader. Copy X's death was covered up, as the humans revered him as their savior.
 * The Resistance is now being led by a Reploid named Elpizo, while Ciel continues her work on a new form of energy that will hopefully eliminate the need for war.
 * Zero wearily makes his way through a sandstorm wrapped in a tattered cloak. As the sands die down he is once more being chased by enemies. Despite being in disrepair, with cracked armor and broken weapons, he charges into the fray.
 * After the battle, Zero collapses from exhaustion and is found by Harpuia.
 * Wishing to see Zero die in battle rather than perish from exhaustion, Harpuia rescues Zero and covertly delivers him to a location near the Resistance base, where he is found and repaired. He learns that Elpizo is planning a frontal assault on Neo Arcadia, as he doesn't believe in Ciel's plan of creating energy as means to resolve the war. Unable to convince him to call it off, Zero is left to do busy-work in the meantime.
 * Elpizo's assault fails miserably, himself being the only survivor. Driven mad, he declares his desire to harness the power of the legendary Dark Elf to destroy Neo Arcadia (and wipe out the humans), which had brought about the Elf Wars a century ago that left the Earth in a disastrous state. Using the powers granted by partially unsealing the Dark Elf, he invades Neo Arcadia and breaks into the temple where the body of the real X is kept.
 * It is revealed that X ended the Elf Wars by sealing the Dark Elf away with his body, thus leading to his disappearance. Despite the Guardians' and Zero's best efforts, Elpizo destroys X's body, which unseals the Dark Elf, and Elpizo absorbs its powers.
 * After a fierce battle, Zero puts an end to Elpizo's plans, who reverts to his normal self and apologizes as he dies. Surprisingly, the Dark Elf turns him into a Cyber-elf, convincing Elpizo that she is not truly evil.
 * As the Dark Elf departs, X appears and tells Zero about the Dark Elf: she was originally known as the Mother Elf and was the savior who ended the Maverick Wars, but was later cursed by a man named Dr. Weil. Zero admits to feeling like he knows her.
 * Sometime later, an unknown man notes the Dark Elf has been released, and tells an entity known as "Omega" that it is time to take action.

Volume 3

 * Two months following Zero's victory over Elpizo, the Dark Elf remains at large.
 * During this time, Ciel has finished her research on a new energy supply to end the crisis, dubbed the "Ciel System". While en route to Neo Arcadia to propose the Ciel System in hopes of ending the conflict and the genocide of Reploids, a spaceship with the Dark Elf's energy reading crashes to Earth.
 * Zero sets out to investigate, but instead finds the remaining Guardians (Harpuia, Fefnir, and Leviathan) fighting against a gigantic Reploid named Omega and a scientist named Dr. Weil — both who were banished to space due to their crimes in instigating the Elf Wars and turning the Mother Elf into the Dark Elf a century prior.
 * Dr. Weil reveals he has resurrected Copy X, who resumes his rule over Neo Arcadia, much to Harpuia's chagrin.
 * The Guardians, suspecting that Copy X is being heavily influenced by Dr. Weil, defect from Neo Arcadia.
 * Zero and Dr. Weil go their separate ways in search of the Dark Elf.
 * The Dark Elf appears in a human residential district in Neo Arcadia, leading Dr. Weil and Copy X to launch a missile in order to incapacitate it. Although successful in capturing the Dark Elf, the incident kills thousands of humans.
 * Following this event, Ciel rescinds her offer of the Ciel System, leading Dr. Weil and Copy X to brand the Resistance as Mavericks and subsequently launch an invasion against them.
 * The Resistance is able to delay the invasion until Zero locates Copy X.
 * During the ensuing battle, Copy X is betrayed and killed by Dr. Weil, who declares himself the new ruler of Neo Arcadia and announces his true intention for capturing the Dark Elf: to fuse it with Omega and link them with a frequency transmitter that would enable Omega to control the minds of every Reploid on Earth.
 * Zero confronts and defeats Omega, who reveals his true form: a body that looks exactly like Zero.
 * Dr. Weil reveals that while Zero was powered down during his 100-year hibernation, he had transferred Zero's conscience and memories to a copy body and stole Zero's original body to be used by Omega due to its unmatched fighting abilities. Despite this revelation, Zero and the Guardians destroy his original body, killing Omega for good.
 * Omega's death results in a massive explosion, which frees the Dark Elf from Dr. Weil's corruption, but kills Harpuia, Fefnir and Leviathan.
 * While Zero is unconscious, X appears and tells Zero that it's up to him to protect the Earth and defeat Dr. Weil.
 * Finally out of power, X vanishes forever. The Dark Elf, known as the Mother Elf once more, delivers Zero to the Resistance Base before flying away.

Volume 1

 * Based on Mega Man Zero.

Volume 2

 * Based on Mega Man Zero 2.

Volume 3

 * Based on Mega Man Zero 3.