Zero manages to stop Elpizo from unleashing the Dark Elf on the world
One year has passed since Zero defeated X. He has since spent his time wandering the desert defeating multiple Pantheons.
Zero wearily makes his way through a sand-storm 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 once again charges into the fray.
mega man Zero Fight eventually collapses from exhaustion after defeating a mechanical scorpion boss, and is found by Harpuia, one of the three surviving members of the Four Guardians
(Phantom self-destructed trying to stop Zero's assault on Area X in the first mega man Zero Fight).
The three 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 into a new form of energy that will hopefully eliminate the need for war.
Wishing to see Zero die in battle rather than perish from exhaustion, Harpuia saves Zero and covertly delivers him to a location near the Resistance base,
where he is soon found by the Resistance and is repaired. He learns that Elpizo is planning a frontal assault on Neo Arcadia,
as he doesn't believe in Ciel's plan of using a new form of 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, with himself as the only survivor.
Driven mad by this, he declares his desire to harness the power of the legendary Dark Elf,
which had brought about the Elf Wars a century ago that left the Earth in a disastrous state.
Elpizo, using the powers granted by unsealing a portion of the power of the Dark Elf,
invades Neo Arcadia and single-handedly breaks into the temple where the body of the real X, revered by all in the utopia, is kept.
It is revealed that X had ended the Elf Wars by sealing most of the Dark Elf away with his body, thus leading to his disappearance.
Despite the Four Guardians' and Zero's best efforts, Elpizo succeeds in destroying X's body, which unseals the Dark Elf, and Elpizo begins to absorb its powers.