The Great Monster Wars were a massive war between Goddess Ilias and Alice I (First) that occurred a thousand years prior to the game's events. According to Luka it is a widely known event, though it is only described by vague legends and no one except its participants know what had actually happened. It is briefly mentioned once in Chapters 1 and 2, and frequently stated in Chapter 3, where Micaela reveals its history.
Several hundred million years ago, Goddess Ilias, the manifestation of light itself, tried to escape her loneliness. She created angels as offshoots of herself, but unsatisfied with her creation, she came to a world and modified its primitive creatures, eventually creating humans. At the same time, Alice I, the manifestation of darkness itself, descended to the same world and created monsters, at a much faster and more controlled rate than Ilias.
Around a thousand years ago, out of jealousy of her power, Ilias and her angels declared war on Alice I and her monsters. The angels Micaela and Lucifina showed their might on the battlefield, and frequently locked in combat with the monstrous Six Ancestors. The daughter of Alice I, Alice II (Second), is also said to have commanded her right hand, Gargoyle Girl, to watch over the Heaven’s Gate.
According to Micaela, the monster forces were superior, but as the war reached its climax the two deities realized that their constant clashing would destroy the world they had created. While Alice I hesitated, Ilias had continued her onslaught, threatening the existence of the world and their creations. Refusing to surrender, Ilias proposed that if Alice I and her Six Ancestors would seal themselves, she would not harm their monsters, effectively using the entire world as a hostage. Seeing no other option, the monster leaders were forced to comply, and had sealed themselves in a special seal known as the Six Ancestors' Great Seal. However, should Ilias break her promise and commit genocide on the monsters, their mass of darkness would be released into the atmosphere and imbalance the world's light and dark magic, resulting the seal breaking.
In the aftermath of the war, Ilias had no intentions of keeping her promise, scheming to eliminate the monsters while keeping her main enemy sealed away. To this end, she had recruited Black Alice, a descendant of Alice I with an intense desire to rule the world, and Promestein, the creator of the artificial monster race chimera, to keep the darkness in check. Ilias additionally eliminated or altered several unfavorable facts from the war, such as removing the existence of the Six Ancestors and Alice I. However, some of Ilias followers began to question her, and ultimately Lucifina and later Micaela rebelled.
Meanwhile, Alice I secretly instructed one of the Six Ancestor, Tamamo, to monitor her descendants from the shadows. As the Great Seal's level of power and effectiveness grows based on the target's strength, Tamamo had thrown her main body into subspace and implanted her spirit into a weaker body, thus rendering her 'immune' to the seal but with a drastic loss in power.
- During Luka's first visit in San Ilia, Priest A briefly mentions the war, stating that traces of the conflict can be found throughout the land.
- It is unknown if Sphinx, who existed a thousand years prior, had any involvement in the Great Monster Wars.
- The Giganto Weapon is a chimera said to have been created during the Great Monster Wars. However, it is not known who had created her.
- Strangely, while Micaela claims that the monster forces were superior, the angels in present day cannot be harmed by any non-holy power; it is not known how the monsters in this war were able to harm the angels. On the other hand, in present day, Alice claims to have scarred Ilias with a punch using the power of darkness, although Torotoro's blog claims that Alice was holding the Angel Halo's hilt as she punched Ilias.
- According to Torotoro's blog, the angels during the Great Monster Wars were vulnerable to attack at the time, although no further explanation was given.