User blog comment:BlackTempest/The Human-Faunus War/@comment-16763585-20131005205222

It sounds like the war was fought over a land dispute. Humans were pressuring Faunus to migrate to a island, likely under threat of hostilities and the Faunus resisted. The Faunus were made to move by force, but thanks to some clever manipulation on their part, they were able to grind a lot of Human rescourses away in the skirmishes. In the end the Faunus were able to propose a conditional surrender, not having the means to gain a victory, and worked out a comprimise between the nations.

Now what Humans wanted with that land is another story. Maybe it was the site of a good Dust quarry, or farming land, or whatever.