On August 5, 1836, he was appointed adjutant general by Thomas Jefferson Rusk and on January 31, 1837, he became senior brigadier general in command of the army to replace Felix Huston. A duel with Huston resulted; Johnston was wounded and could not immediately take the command. On December 22, 1838, he was appointed secretary of war for the Republic of Texas by President Mirabeau B. Lamar, and in December 1839 he led an expedition against the Cherokee Indians in East Texas. On March 1, 1840, Johnston returned to Kentucky, where, on October 3, 1843, he married Eliza Griffin, a cousin of his first wife. They returned to Texas to settle at China Grove Plantation in Brazoria County.
During the Mexican War he was colonel of the First Texas Rifle Volunteers and served with W. O. Butler as inspector general at Monterrey, Mexico. On December 2, 1849, Johnston became paymaster in the United States Army and was assigned to the Texas frontier. He went with William S. Harney to the Great Plains in 1855, and on April 2, 1856, he was appointed colonel of the Second Cavalry. In 1858 Johnston received command of a Utah expedition to escort a new territorial governor and three judges to Salt Lake City and to establish a military presence, due to Mormon resistance of federal authority. He set up Camp Scott near the ruins of Fort Bridger in the fall of 1858, and later selected a site southwest of Salt Lake City for a permanent camp - Camp Floyd which was dedicated in November of 1859. Johnston remained in charge of Camp Floyd until 1860 when he was sent to the Pacific Department and stationed at San Francisco. At the beginning of the Civil War in 1861, he resigned his commission in the United States Army, refused the federal government's offer of a command, and returned overland to Texas.
In Austin 1861 Jefferson Davis appointed Johnston a general in the Confederate Army and in September assigned him command of the Western Department. Johnston issued a call for men and formed and drilled an army, but it lacked men and organization, had a huge area to defend, and could not control the rivers that were vital to military success in the region. In February 1862, following Federal victories on the Cumberland and Tennessee rivers, he moved his line of defense to the vicinity of Nashville, Tennessee, and later to Corinth, Mississippi. On April 6, 1862, he was killed while leading his forces at the battle of Shiloh. He was temporarily buried at New Orleans. By special appropriation, the Texas Legislature, in January 1867, had his remains transferred to Austin for burial in the State Cemetery. In 1905 a stone monument executed by noted sculptor Elisabet Ney was erected at the site.
30° 15.913, -097° 43.597
Texas State Cemetery