During the American Civil War, Army reorganization created the Department of the Pacific on 15 January 1861, and on 12 December 1861, the Humboldt Military District, which was formed to organize the effort to unseat the native population.

The hunting and gathering economy of the Bald Hills tribes that had previously satisfied their wants was increasingly disrupted following the Klamath and Salmon River War in 1855.

From 1856 onward thousands of acres of native lands were preempted for the growing of wheat, oats, barley and potatoes and for grazing of cattle or pigs.

For the Whilkut the surge in settlement by cattle and hog raising settlers into their lands in the Bald Hills, and the loss of the game, acorns and other plant foods they depended on, caused a feeling of hatred against them and a desire to drive them from the country.

On July 1, 1858, three parties of volunteers were organized for a campaign against the Indians on Redwood Creek and Upper Mad River, in the vicinity of Pardee's Ranch.

Following the failure of these local militia parties, in late August 1858, citizens of the Bay towns of Union and Eureka agitated for the regular formation of Volunteer Companies, and raising money to defray their expenses.

Public meetings of the citizens of Union and Eureka were held for the purpose of considering and adopting some method of protection to life and property during the continuance of the war with the Whilkut.

The Governor requested Adjutant General Kibbe to proceed to Weaverville and make a detailed report of conditions in that region, to ascertain the number of Indians in the vicinity, and the character of the outrages that were committed by the hostiles.

However, on 26 February 1860 some settlers lashed out at the peaceful coastal Wiyot people in a series of killings around Humboldt Bay including the Indian Island Massacre.

Elements of California Volunteer Regiments raised to replace Federal troops during the Civil War were sent to the newly formed Humboldt Military District under Col. Francis J. Lippitt.

They established a number of posts to protect the settlers, but the troops raised outside the rugged Northwest were at first unsuited to conditions there, and failed to defeat the native peoples.

Under his command of the Humboldt District he began a more active campaign of unrelenting extended patrolling and skirmishing by all the units of California Volunteer soldiers.