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Near the end of the Maverick Wars, Dr. Weil, one of the humans researching ways to eradicate the Maverick Virus, proposed “Project Elpizo”, an operation to create a Reploid that’s a perfect ruler using the Sigma Antibody program, the "Mother Elf". Mega Man X opposed this project, but out of fear of another long-lasting war, humans started to build up support for complete control of Reploids. The human leadership’s “philosophy of rule” conflicted with X’s “philosophy of coexistence”. This would only lead to the worst war in history, the Elf Wars, when Dr. Weil used Baby Elves to completely control Reploids at will and make them fight amongst themselves. Concerned over the Elf Wars himself, X formed the "Neo Arcadia" organization for the sake of providing protection for the humans. Rather than exercising control by using the Dark Elf, X successfully used his "reputation" to invoke order.
At the closing of the Elf Wars, Dr. Weil completed Omega, but was unable to complete Project Elpizo since Zero had returned and captured the Dark Elf. Omega ended up betraying the human leadership under Dr. Weil's orders and attacked both humans and Reploids alike. Though he had an army of Neo Arcadia's great Mechaniloids Golem by his side, Omega was defeated by X and Zero while the Reploids controlled by the Dark Elf returned to normal, putting an end to the war. 
In the aftermath, Omega was sent into space, and Weil was banished from Neo Arcadia as a criminal. At that time, deceiving the whole world to protect their reputation, the pro-mankind utopia nation buried the "human" Weil's grave sin into history's darkness without revealing it. After a very long time, even Neo Arcadia entirely forgot about the risks Weil took.
100 years later, Neo Arcadia organized the Administration Bureau and the Hunters to conduct a large scale survey into a newly-discovered information facility from the previous age; the Sunken Library. The survey was supervised on-site by Sage Harpuia as X's administration from the scientific branch. Though Harpuia's orders were to avoid independent action and report any situations to the accompanying Hunters, a Reploid of the administration bureau, TK-31, wandered off on his own. As if guided by something, he ended up in the deepest data room. There he discovered fragments of history sealed away in the darkness, information he had never heard of or seen before and he was completely enthralled. Through seeing a record, the truth would spread out unbidden before his eyes. TK-31 saw the power that nearly led the world to destruction, Dark Elf; the above-first-degree war criminal Dr. Weil; the end of the Elf Wars; the operation to completely control Reploids, and X fighting alongside others against Omega. Seeing these events reminded him that the research facility in Area 7 stores the Baby Elves from the time of the great war. An alarm went off and the record rewound itself in overflow. Subjected to all this information, TK-31 saw the Maverick Wars, the Sigma Antibody Program Mother Elf, her light saving the world; calling it the birth of hope, he mistakenly concluded: "This is Project Elpizo". Hearing the alarm, Harpuia arrived on the scene and ordered TK-31 to forget everything that he saw.
During the following week, Neo Arcadia made the energy distribution quotas for the serial-number Reploids stricter and the Maverick arrest rate rose with an unprecedented 8%. Amongst the Reploids there was a lot of talk that there were no abnormalities in the group that was retired and that another group managed to escape and staged an armed uprising, forming a Resistance. Meeting with HE-22, another Reploid of the administration bureau, TK-31 learned about this situation and is informed that mysterious and dangerous things are happening to the Reploids involved in the survey and that the submerged city was deleted from the records. Before HE-22 could get his entire point across, the Hunters showed up and designated TK-31 as a Maverick. Caught by complete surprise, TK-31 was forced to flee HE-22, who revealed himself as a member of the Resistance trying to recruit TK-31 as an indispensable ally in helping free his comrades who would be retired under false pretenses. Though TK-31 agreed to join the Resistance, he insisted on first wanting to figure out what was going on in the research facility in Area 7. HE-22 was reluctant and tried to talk TK-31 out of it, to which TK-31 however responded that HE-22 should stop calling him by his serial number. Declaring that his name is really "Elpizo", after the project mentioned in the records, he ironically proclaimed that he was chosen to become the hope of all the Reploids oppressed in Neo Arcadia, unaware of what Project Elpizo really stood for.
Afterward, Elpizo became the leader of the Resistance. However, a crushing defeat at the Four Guardians' hands left him craving for more and more power. Eventually seduced by the power of the Dark Elf, Elpizo ended up breaking the Dark Elf's seal, and setting in motion a chain of events that allowed Dr. Weil and Omega to return from exile, once more scheming to control all Reploids. Though Weil initially once more used the Baby Elves, they were no longer needed once Omega managed to capture the Dark Elf and became "absolutely perfect". Using Omega and Dark Elf, Dr. Weil brainwashed all the world's Reploids. However, Omega's brainwashing had no effects on X, Zero and the Four Guardians, who joined forces against Dr. Weil and Omega.
Though successful in destroying Omega and stopping Weil's scheme, the Four Guardians gave up their lives, and X has used up all his energy, unable to manifest in the physical world any longer. Dr. Weil is still alive and rules Neo Arcadia, and all hope in ending his reign of terror lies in Zero.
- ↑ Rockman Zero Collection official site: []
- ↑ Mega Man Zero 3
- ↑ Mega Man Zero Complete Works, Three Keys to Solving the Mystery of Zero and Omega, Elf Wars
- ↑ Vile's Incident, Eden Dome its sin and rebirth
- ↑ Remastered Tracks Rockman Zero - Telos (Record1: Clockwork Apple)
- ↑ Remastered Tracks Rockman Zero - Telos (Record2: Irregular Passion)
- ↑ Mega Man Zero 3