The group was to protect the Methodist Mission there and prevent any hostile forces from reaching the Willamette Valley. While preparation were made for war, the Provisional Government also attempted to negotiate with the Cayuse and other tribes. Lee was appointed as one of the peace commissioners, along with Joel Palmer and Robert Newell to seek a truce with the Cayuse and demand they turn over the killers from the massacre at the start of hostilities. Lee and his troops, with John E. Ross and Joseph Magone as lieutenants, then marched off to The Dalles, arriving on December 21. Upon arriving there, Lee led his men against a band of Native Americans and drove them off, but not before they stole 300 head of cattle. There the troops built a stockade and named the post Fort Lee for the commander, though the small fortification was also called Fort Wascopam. Lee's forces continued defending the Wascopam Mission and settlers until Colonel Cornelius Gilliam arrived with a larger force in February 1848, at which point Lee became third in command after Gilliam and Lieutenant-Colonel James Waters. With a larger force, the militia forces pressed east towards the Whitman Mission, with Lee commanding some troops and carrying out reconnaissance. By March 4 the forces reached the mission after a battle at Sand Hollows. After reaching the mission, Gilliam set out for The Dalles with a small force to supply that settlement, before continuing to Oregon City to report to the governor when he was accidentally shot and killed. Lee continued west with Gilliam's body and was promoted to Colonel before returning to the front. Once at the front he discovered that the troops had elected Waters as Colonel, so Lee resigned as colonel and took the role as a subordinate to Waters. After leaving the war, Governor Abernethy appointed Lee as superintendent of Indian Affairs in 1848. In 1849, he sought his fortune in the gold mines of the California Gold Rush. He successfully mined there before returning to Oregon and setting up business in Oregon City in 1850. That year Lee traveled by ship to New York to acquire inventory for his store, but died of Panama fever on his return to Oregon in 1851.