Whipple's party made good progress through Indian Territory (now Oklahoma), the Texas panhandle and the New Mexico Territory, reaching Albuquerque on October 5. After Albuquerque, they were joined by frontiersman Antoine Leroux who helped to guide the surveyors through the most difficult part of the journey to California. They reached California on February 7 after a near-disastrous crossing of the Colorado River then crossed the Mojave Desert and reached Los Angeles on March 20, 1854. The findings of the Whipple expedition along with the other transcontinental survey parties were published by the government in a massive twelve-volume report, the "Pacific Railroad Reports". In addition to reports on topography, geology, botany and zoology, Whipple wrote a lengthy essay on the southwestern Indian tribes that the expedition had encountered. Whipple was promoted to captain in 1855 and then assigned to supervise efforts to open the Great Lakes to navigation by larger vessels, deepening channels through the St. Clair flats and the St. Mary's River. He was also commander of the lighthouse districts from Lake Superior to the Saint Lawrence River. At the outbreak of the Civil War, Whipple served for a time under General Irvin McDowell as commander of the nascent balloon reconnaissance unit. He made a balloon ascent over the Confederate lines at Bull Run. He then became chief topographical engineer under General George B. McClellan in the Army of the Potomac. His maps were used on many Virginia battlefields. In 1862, as brigadier general of volunteers, he led the defense of Washington, D.C., on its Virginia side. In September 1862 Whipple was assigned to the Third Army Corps, and on December 13–15 participated in the Battle of Fredericksburg. Whipple was severely wounded by a sharpshooter at Chancellorsville on May 4, 1863, received last rites on the battlefield and was taken to Washington. Just before Whipple's death on May 7 President Lincoln, a friend of Whipple's, promoted him to major general of volunteers. Lincoln rode in an open carriage as part of Whipple's funeral cortege. He was later awarded posthumously more brevets for his wartime services, and both of his sons received presidential appointments to the military academy of their choice. He was buried in the Proprietors' Cemetery, Portsmouth, New Hampshire. Whipple was memorialized with the naming of two forts, Fort Whipple, Arizona Territory and Fort Whipple, Arlington County, Virginia (now Fort Myer).