The War of Independence is a war which started in the year 458 of the Unified Era. It began when Athos, Certes and Thena, three of the Northern Kingdoms, attempted to cede from the rest of Imperia. Elyria was one of the other countries most involved in the war. The allied nations (Athos, Certes and Thena) launched a pre-emptory strike against Elyria, and gained quite a bit of territory. However, the Elyrians were quite certain they would regain that territory quite easily.

Each kingdom had a different reason for joining the Allied force. Certes is a kingdom which follows a single-god religion, and they were hoping to unite Imperia under that religion. Thena is a small kingdom with little room for development, so they joined the war in the hopes of gaining more territory. Athos probably wanted more land, since the land was not right for agriculture.

The war is how Aeron, the main protaganist of Pandora's Tower, met Elena. Aeron was an Athosian soldier, but he was wounded during one of the raids on an Elyrian village in 508. Running away from the village, he tripped over and fell, falling unconscious. Luckily, he was close to Elena's village, located near the city of Helycon. She found him unconscious and took him back to her house. Since then Aeron has been living with her, despite the hostility between their home countries.

In the year 509, Elyria offered a peace treaty to Athos, which the Kingdom would not accept. The fighting continued, but not as heavily; there were just some skirmishes near the border of Elyria.