After gold was discovered in California, Cornelius journeyed there for a brief time, returning to the Oregon Territory in 1849. The next year, he married Florentine Wilkes, and they had six children together before she died in 1864, including son Benjamin. The family would settle on of their Donation Land Claim near Cornelius. In 1855, a second war against the Native Americans started east of the Cascade Mountains against the Yakima tribe. Cornelius volunteered again for the militia. For three months, he led a company with the rank of captain before being elected as colonel after James W. Nesmith resigned his commission. Cornelius continued as colonel until the end of the war in 1856.During this campaign, his troops waged war indiscriminately against any natives found in the area. In one case, a Nez Perce native was accused of being a spy and summarily hanged, which alarmed members of the U.S. military.