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This Civil War (c. 1027 AG - 1099 AG) was conducted between the usurpant House of Feyd and those loyal to the House Corrino including the Sardaukar. Atreides took a large part in the opposition, since usurper Feyd I was a member of the House Harkonnen
tried to organize a resistance to his rule and Feyd branded them as traitors. They were joined by rebel Sardaukar
Paulos, attainted, stripped of all titles and lands and condemned to death on sight, fled beyond the bounds of the Imperium with the last survivors of the Imperial House including Prince Corrin and his son, 5-year old Josif I. They conducted various battles against the Imperial forces with very little gain. In 1044 AG Feyd made a surprise attack on rebel headquarters, where Paulos was killed but Alexios, while still underage, escaped with Prince Corrin.
After Feyd's death in 1051 AG, Estil II continued the war against the loyal to the throne until it degenerated into stalemate. Rebels controlled the outer colonies and the Imperial Fleet controlled the main trading worlds. The Guild sold transport to both sides but in 1096 AG Odusseus Atreides bought the assistance of the Guild for a surprise raid on Ibleam III and Ibleam IV which marked the beginning of the end for the Feyd regime; soon the Imperial forces began losing ground and By 1099 AG only a few worlds remained in Imperial control, the most being captured by rebel, loyal to the House Corrino.