Still only in his early mid-30s at the time, Fremont had already won national acclaim for his leadership of two important explorations of the West with the military's Corps of Topographical Engineers. Shortly after the government published Fremont's meticulously accurate maps of the Far West, they became indispensable guides for the growing numbers of overland emigrants heading for California and Oregon. In 1845, though, the lines between military exploration and military conquest began to blur when President James Polk sent Captain Fremont and his men on a third "scientific" mission to explore the Rockies and Sierra Nevada—with 60 armed men accompanying them. Polk's ambition to take California from Mexico was no secret, and Fremont's expedition was clearly designed to place a military force near the region in case of war.
When Mexico and the U.S. declared war in May 1846, Fremont and his men were in Oregon. Upon hearing the news, Fremont immediately headed south, calling his return "the first step in the conquest of California." When the Anglo-American population of California learned of Fremont's arrival, many of them began to rebel against their Mexican leaders. In June, a small band of American settlers seized Sonoma and raised a flag with a bear facing a five-pointed star—with this act, the revolutionaries declared the independent Republic of California.
The Bear Flag Republic was short-lived. In August, Fremont and General Robert Stockton occupied Los Angeles. By January 1847, they had put down the small number of Californians determined to maintain a nation independent of the United States. With California now clearly in the U.S. hands, Stockton agreed to appoint Fremont as the territorial governor. However, a dispute broke out within the army over the legitimacy of Fremont's appointment, and the young captain's detractors accused him of mutiny, disobedience, and conduct prejudicial to military discipline. Recalled to Washington for a court martial, Fremont was found guilty of all three charges, and his appointment to take the position of governor was revoked. Though President Polk pardoned him and ordered him back to active duty in the army, Fremont was deeply embittered, and he resigned from the military and returned to California a private citizen.
Although he never regained the governorship of California, the turmoil of Fremont's early political career did not harm his future prospects. In 1851, citizens of California elected him a senator, and became the territorial governor of Arizona in 1878. Today, however, Fremont's youthful accomplishments as an explorer and mapmaker are more celebrated than his subsequent political career.