Drake served as an officer in both the 1st Oregon Cavalry and 1st Oregon Infantry volunteer regiments during the Civil War. When the American Civil War began, he volunteered for service in the
United States Army. On November 29, 1861, Drake was commissioned as a first lieutenant in the 1st Oregon Cavalry. He was quickly promoted to captain, taking command of the cavalry regiment's D Company. Drake and several other cavalry officers led lengthy explorations through
eastern Oregon, northern
Nevada, and southwestern
Idaho searching for
Indian raiders. Most of these patrols were unsuccessful in finding hostile Indians. However, Drake was involved in several minor skirmishes. In May 1864, Drake was leading several companies of cavalrymen in the upper
Crooked River area of eastern Oregon. The expedition was in response to Chief Paulina's raids on settlers and rival Indians in that region. Late in the evening of May 17,
Warm Springs Indian scouts working with the 1st Oregon Cavalry found Chief Paulina's camp about twelve miles from Drake's camp, a site that later became Camp Maury. Before dawn the next morning a small group of soldiers and Warm Springs Indian scouts led by Lieutenant
Stephen Watson attacked Paulina's camp from three sides. Chief Paulina and his men quickly retreated to a rocky cliff. In the ensuing battle, Lieutenant Watson, two soldiers, and several Indian scouts were killed. Before Drake's main force could reach the site of the battle, Paulina escaped leaving behind three dead. During an expedition to resupply Army posts in eastern Oregon, Drake discovered
fossilized bones in the hills southwest of Sheep Rock in the upper John Day basin. On July 19, 1864, Drake wrote to
Thomas Condon about his discovery. On his way back to
Fort Dalles, Drake loaded empty wagons with fossils to deliver to Condon. Condon, a pastor living at Fort Dalles, had an active interest in the natural sciences. Based on Drake's directions, Condon explored the area that is now the
John Day Fossil Beds National Monument. In late 1864, Drake was promoted to lieutenant colonel and transferred to the newly established 1st Oregon Infantry as the regiment's second highest-ranking officer. While some detachments of the 1st Oregon Infantry occasionally skirmished with hostile Indian bands, most companies spent their time in garrison duty at small posts in eastern Oregon, southeast
Washington, and southern Idaho. They protected immigrant trails and escorted wagon trains from
Fort Boise to the
Willamette Valley. Two companies escorted survey parties; and another, led by Captain
Franklin B. Sprague, constructed a road in southwestern Oregon. In the fall of 1865, Drake's regiment was planning a winter campaign against the Indians in eastern Oregon. However, the end of the Civil War in the east had freed up many regular officers for duty in the west. As a result, most of the volunteer officers and men of the 1st Oregon Infantry regiment were released from service in November, so the planned winter campaign never got started. Drake was mustered out of the Army a month later, in December 1865. == Later career ==