U.S. Army Service
Johnston resigned from the Army in March 1837 and studied civil engineering. During the Second Seminole War, he was a civilian topographic engineer aboard a ship led by William Pope McArthur. On January 12, 1838, at Jupiter, Florida, the sailors who had gone ashore were attacked and Johnston was to claim there were "no less than 30 bullet holes" in his clothing and one bullet creased his scalp, leaving a scar he had for the rest of his life. Having encountered more combat activities in Florida as a civilian than he had had previously as an artillery officer, Johnston decided to rejoin the Army. He departed for Washington, D.C., in April 1838 and was appointed a first lieutenant of topographic engineers on July 7; on that same day, he received a brevet promotion to captain for the actions at Jupiter Inlet and his explorations of the Florida Everglades.
On July 10, 1845, in Baltimore, Johnston married Lydia Mulligan Sims McLane (1822–1887), the daughter of Louis McLane, the president of the Baltimore and Ohio Railroad and a prominent former politician (congressman and senator from Delaware, minister to London, and a member of President Andrew Jackson's cabinet). They had no children.
Johnston was enthusiastic about the outbreak of the Mexican-American War. He served on the staff of Lt. Gen. Winfield Scott in the Siege of Veracruz, having been chosen by Scott to be the officer carrying the demand for surrender beforehand to the provincial governor. He was in the vanguard of the movement inland under Brig. Gen. David E. Twiggs and was severely wounded by grapeshot performing reconnaissance prior to the Battle of Cerro Gordo. He was appointed a brevet lieutenant colonel for his actions at Cerro Gordo. After recovering in a field hospital, he rejoined the army at Puebla. During the advance toward Mexico City, he was second in command of a regiment of U.S. "Voltigeurs", meaning light infantry or skirmishers. He distinguished himself at Contreras and Churubusco, was wounded again at Chapultepec, and received two brevet promotions for the latter two engagements, ending the war as a brevet colonel of volunteers. (After the end of hostilities, he reverted to his peacetime rank of captain in the topographical engineers.) Winfield Scott remarked humorously that "Johnston is a great soldier, but he had an unfortunate knack of getting himself shot in nearly every engagement." Despite his wounds, however, Johnston's greatest anguish during the war was the death of his nephew, Preston Johnston. When Robert E. Lee informed Johnston that Preston had been killed by a Mexican artillery shell at Contreras, both officers wept, and Johnston grieved for the remainder of his life.
Johnston was an engineer on the Texas-United States boundary survey in 1841 and returned to be chief topographical engineer of the Department of Texas from 1848 to 1853. During the 1850s he displayed an early indication of his sensitivity for rank and prestige, sending letters to the War Department suggesting that he should be returned to a combat regiment with his wartime rank of colonel. Secretary of War Jefferson Davis, an acquaintance of Johnston's from West Point, rebuffed these suggestions, a practice that he would continue during the Civil War, much to Johnston's irritation. Despite this disagreement, Davis thought enough of Johnston to appoint him lieutenant colonel in one of the newly formed regiments, the 1st U.S. Cavalry at Fort Leavenworth, Kansas, under Col. Edwin V. "Bull" Sumner, on March 1, 1855. (At this same time, Robert E. Lee was appointed lieutenant colonel of the 2nd U.S. Cavalry under Col. Albert Sidney Johnston (no relation).) In this role, Johnston participated in actions against the Sioux in the Wyoming Territory and in the violence known as Bleeding Kansas. He developed a mentor relationship and close friendship with one of his junior officers, Capt. George B. McClellan, who would become one of his principal opponents during the Civil War.
In the fall of 1856, Johnston was transferred to a depot for new recruits at Jefferson Barracks, Missouri. In 1857 he led surveying expeditions to determine the Kansas border. Later that year, a new Secretary of War replaced Jefferson Davis—John B. Floyd, a native of Abingdon, a cousin of Johnston's by marriage, and former guardian of Preston Johnston. Floyd overturned Davis's previous decision about Johnston's highest brevet rank and he was listed as a brevet colonel for Cerro Gordo, an action that caused grumbling within the Army about favoritism. In 1859, President James Buchanan named Johnston's brother-in-law, Robert McLane, as minister to Mexico, and Johnston accompanied him on a journey to visit Benito Juárez's government in Veracruz, ordered to inspect possible military routes across the country in case of further hostilities.
Brig. Gen. Thomas S. Jesup, the Quartermaster General of the U.S. Army, died on June 10, 1860. Winfield Scott was responsible for naming a replacement, but instead of one name, he offered four possibilities: Albert Sidney Johnston, Joseph E. Johnston, Robert E. Lee, and Charles F. Smith. Although Jefferson Davis, now a member of the Senate Military Affairs Committee, favored Albert Sidney Johnston, Secretary of War Floyd chose Joseph E. Johnston for the position. Johnston was promoted to brigadier general on June 28, 1860. Johnston did not enjoy the position, preferring field command to paperwork in Washington. In addition, he suffered from the pressures of the imminent sectional crisis and the ethical dilemma of administering war matériel that might prove useful to his native South; he did not yield to temptation, however, as Secretary of War Floyd was accused of doing.
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