The Aetherium Wars was a massive civil war that took place during the First Era; it was an internal conflict within the Dwemer civilization. The wars that took place was a result of the Dwemer civilization fighting over the control of Aetherium resources, the Aetherial artifacts and the Aetherium Forge itself.
During the First Era, as the Dwemer were still mining in Blackreach, they discovered a new, peculiar mineral which they called Aetherium. Immediately, an alliance was made between four cities: Arkngthamz, Raldbthar, Mzulft, and Deep Folk Crossing/Bthar-zel. Arkngthamz was assigned the role as the primary command and research center, to oversee the Aetherium's extraction, processing and study  , while Mzulft was used as a storage site and with Raldbthar being used as the primary source of Aetherium, which came directly from Blackreach (Raldbthar was located directly above the main entrance to Blackreach).  The Aetherium Forge was built deep beneath Bthalft; the city of Bthalft and the Aetherium Forge are over 4,000 years old, ancient even by Dwemer standards. The results of the Aetherium project were "nothing short of spectacular;" the Aetherial artifacts which were created by the Aetherium Forge were incredible artifacts with immense power. 
The War BeginsEdit
In just a short amount of time, the four city-states that participated in the Aetherium project attempted to take control of the Forge, each for their own. Civil war erupted and a new conflict emerged in the history of Tamriel and of the Dwemer civilization: the Aetherium Wars. Quickly, war spread across Skyrim, and decades of conflict began to weaken the Dwemer city-states of Skyrim. 
The Rise of High King GellirEdit
A century later, the Dwemer civilization would recover and reclaim most of their cities and territory which they had previously lost. The Aetherium project was most likely not continued, as the costs were too great, and there is no evidence that they ever resumed the project.