Ikaruga Civil War

The Second Great Magic War (第二次魔道大戦), also known as the Ikaruga Civil War (イカルガ内戦), was a war that began when the Ikaruga Federation openly rebelled against the dictatorship and governance of the World Void Information Controlling Organization. It is the first time mankind used the Magic Formula against each other, but second overall.

Information
In 2191, when an alliance of five Hierarchical Cities centered around the 5th Hierarchical City "Ibukido" called themselves the Ikaruga Federation, and declared independence. The World Void Information Controlling Organization didn't accept this, and started suppression through force against Ikaruga, which led to the start of the war. Meanwhile, Seventh Agency takes use of the war, and starts the experiment to temper a Black Beast.

After a year, the Ikaruga Civil War expands territories, to which the Controlling Organization declares that it's a war of invasion.

In December 25, 2194, the accident happens. The Ikaruga Federation's center, Ibukido, gets destroyed by the Highlander: Takemikazuchi during the tempering process of Mu-12. In most of the timelines Mu survives thanks to her cocoon, but she loses her memories.

In June 2197, the World Void Information Controlling Organization sent Jin Kisaragi to battle, giving him a unit to commandeer. During this time, Grimwood Hastur, the commander of his department, gets executed for treason by Meifang Lapislazuli of the 0th Division.

Jin decided to take care of the leader of Ikaruga, Tenjō Amanohokosaka, as he believed it would stop the war. When he arrived at the Wadatsumi castle, one of the Amanohokosaka's disciples, the leader of Ikaruga ninjas tried to stop Kisaragi, but he failed. However, he wasn't killed, but left with a cross-shaped scar on his face. Eventually, Jin Kisaragi killed Tenjō Amanohokosaka, and then the Ikaruga people stopped fighting. This was the end of the war, and Jin earns the title of the Hero of Ikaruga.

After these events, the Controlling Organization imposed a much harsher rule in the world: anyone who rebels against them, will automatically be dealt the "death sentence".

There were plenty of others who were capable of ending the war besides Jin Kisaragi, but nearly all of them were charged with false crimes and disposed by the Wings of Judgment. This was done to prolong the war, by eliminating most of those that could have ended it too quickly.

The area, in which the Kaka Village lies, was scheduled to undergo massive development, but the effects of the Ikaruga War resulted in the area being completely abandoned, along with its dwellers. Kokonoe Mercury names the Lost Town as one of the victims of Seventh Agency's selfishness.

War reasons
The Ikaruga Civil War was started by Seventh Agency in order to gather necessary ingredients, namely souls, so that they could create the Black Beast and oppose the Controlling Organization. That is why Ikaruga is filled with Kilns, with all of them set up to gather souls.

Further information from Makoto suggests that the Controlling Organization caused the war in the first place, despite the Ikaruga Federation attempting to become independent through diplomacy. She also stated that the Emperor insisted upon the war and refused to accept a ceasefire, with emphasis on inflicting as many casualties as possible.

In reality, this war was plotted for two reasons. The first was an "experiment" requiring the gathering of a massive number of souls, in order to smelt the "Black Beast" once more. The second was the elimination of the "previous Emperor". The third was the desire of Hazama and Relius Clover to collect many deaths to awake Hades: Izanami, the death incarnation.

Hakumen's timeline
In Hakumen's timeline, the region of Ikaruga was annihilated. Takemikazuchi's blast was so powerful, that nothing was left of Ibukido and the surrounding cities. It killed Mu and Tenjō, and Jin didn't became the Hero of Ikaruga. Indifference to the current timeline, it was the destruction that sparked the Civil War. In the end, both sides suffered great losses, with the World Void Information Controlling Organization being recognized as the winner.