Elf Wars

The Elf Wars is an extremely bloody series of battles that marked the closure of the Maverick Wars, one century prior to the events of the Mega Man Zero series. It is considered the worst war in history, and it was named for the exploitation of many Cyber-elves in the conflict. Although the Elf Wars lasted only four years, the casualties were extremely deep: approximately 90% of all Reploids and 60% of all humans were wiped out. The events of the Elf Wars are directly related to the storyline of the Zero games.

Prelude
After X used the Mother Elf to delete the Sigma Virus, the number of Mavericks decreased significantly. It was at this point that the human scientist Dr. Weil proposed Project Elpizo: a plan to control all Reploids by combining the Mother Elf's rewriting abilities with a Reploid created to be a perfect ruler. Although X opposed this operation and Dr. Weil's "philosophy of rule" with his own "philosophy of coexistence", a fear of a long-lasting war resulted in increasing support for Project Elpizo.

To further his own secret agenda of a new world order with him as ruler, Dr. Weil instigated the Elf Wars by stealing the Mother Elf herself and corrupting her with a "curse" that turned her into the Dark Elf. Dr. Weil then created the Baby Elves, infant copies of the Dark Elf which he used to make Reploids turn Maverick and fight each other on a grand scale, plunging the world into chaos. With full support from the human government, Dr. Weil continued Project Elpizo and attempted to exert total control over all Reploids in the world by combining the Dark Elf with the Reploid Omega. Omega was constructed from the body of Zero (who was in stasis at the time) because Dr. Weil believed that a body immune to infection would be the perfect weapon to end the Maverick Wars.

Climax
Zero's brain (or soul) wasn't in his body, and he was given a new body to help in the fight against Weil. X continued to fight in the front lines against Mavericks and deleting the evil Baby Elves, until he was joined by Zero. Together, X and Zero worked to capture the Dark Elf and eventually used her power to turn the tide of the battle. When the war reached its final stretch, Dr. Weil unleashed the completed Omega in the battlefield, revealing his true ambitions to the world. Under Dr. Weil's orders, Omega, supported by an army of Golems, slaughtered countless humans and Reploids alike.

After a long struggle, X and Zero defeated Omega with a Final Strike and Weil was stopped right before he could combine Omega with the Dark Elf, putting an end to four years of devastating conflict.

Epilogue
Although Omega managed to survive the final battle, the "Devil Reploid" was sentenced to perpetual exile on Earth's orbit within the Forbidden Ark, whereas Dr. Weil was punished in a similar yet unprecedented manner: away from public eyes, the human survivors modified Dr. Weil's old body, turning him into a cyborg encased in regenerative armor. Dr. Weil's memories were converted into program data so that he would never forget what he had done, and he was banished, doomed to suffer for eternity in the wastelands of the war.

Even though Zero fought bravely in the wars, he feared that his presence would cause history to repeat itself and willingly returned to stasis. X moved on to create the city of Neo Arcadia (named after the organization from the Elf Wars) to finally bring peace and stability to the survivors. All existing records of the Elf Wars and the crimes committed by Dr. Weil were eventually disposed of in locations such as the Sunken Library in order to protect the reputation of the government of the pro-human utopia. Over time, the people of Neo Arcadia would forget Dr. Weil and his sin, and X continued to govern Neo Arcadia until the day he was forced to sacrifice his own body to keep the Dark Elf sealed in Yggdrasil.

Mega Man (Archie Comics)
The Elf Wars appear briefly for one page in the 55th issue, as one of Dr. Light's visions of the future, showing X, Zero, Axl, and a Cyber-elf Dr. Light in combat against Omega and a horde of Golems, while a younger Dr. Weil and the Dark Elf watch from a nearby clifftop.

Trivia

 * It was mentioned in the Rockman Zero Collection Timeline that many historians define the end of the Maverick Wars as the period when the number of Mavericks dropped significantly due to X’s use of the Mother Elf. However, there was no definite end to the conflict and this the latter period of the Maverick Wars came to be known as the Elf Wars.
 * Information in the Rockman Zero Collection Site revealed that X founded the organization of Neo Arcadia during the Elf Wars to provide protection for the humans, using his reputation to maintain order instead of exercising control by using the Dark Elf. These details were since removed from the site.