At the outbreak of the Civil War, he enlisted on June 16, 1861, in Col. John (Rip) Ford's Second Texas Cavalry regiment. He participated in two actions, the battle of Galveston Bay, where he was wounded, and the Confederate defeat at La Fourche Crossing, Louisiana. On November 26, 1863, he married Catherine L. Moore, the daughter of a prominent Austin merchant, Martin Moore. After his marriage he returned to the army and served till the end of the war. In May 1865 Thompson fatally shot a teamster in Austin after the man pulled out a shotgun during an argument over an army mule. Later arrested by federal soldiers, Thompson broke jail and left the state to join Emperor Maximilian's forces in Mexico. Fighting until the fall of the empire in June 1867, Thompson received several promotions for gallantry in action. He then returned to Texas and slightly wounded his brother-in-law, Jim Moore, who was abusing his pregnant sister, Thompson's wife. Thompson was sentenced on October 20, 1868, to four years' hard labor and sent to the Texas State Penitentiary at Huntsville, where he was held for two years until his conviction by a military tribunal was deemed illegal and he was pardoned by President U.S. Grant. After his release, he left Texas for Abilene, Kansas, undoubtedly hoping to change his fortunes.
In 1871 he opened the Bull's Head Saloon with his Civil War friend, Philip H. Coe. The pair ran the drinking and gambling establishment while Abilene prospered as a railhead for the cattle drives originating in Texas. Thompson was involved in a buggy accident in Kansas City which also injured his son and his wife, who had her arm amputated. While Thompson was recovering, his partner Coe was killed in a shootout with Abilene marshal "Wild Bill" Hickok. In the summer of 1873 Thompson was working as a house gambler in an Ellsworth, Kansas, saloon with his younger brother Billy. On August 15, during a drunken altercation with other gamblers, Billy shot and killed Ellsworth sheriff Chauncey B. Whitney, a friend of the Thompson brothers. Billy Thompson fled Kansas and avoided authorities until 1876, when he was returned to Ellsworth, stood trial, and was acquitted. The jury ruled that the shooting was an accident.
Aside from a visit to Kansas in the spring of 1874, Ben Thompson made his living as a gambler in various Texas cities between 1874 and 1879. On December 25, 1876, Thompson was at Austin's Capital Theatre with several friends when a fight erupted. When Thompson tried to intervene on behalf of one of the troublemakers, theater owner Mark Wilson emerged with a shotgun. In the ensuing fracas, Wilson fired at Thompson and was killed by three fast return shots. Thompson was found to have fired in self-defense. The Leadville, Colorado, silver strike lured Thomson to visit Colorado several times during the spring and summer of 1879. There he joined a group of Kansas gunmen led by Bartholomew (Bat) Masterson who were hired by the Atchison, Topeka and Santa Fe Railway in a right-of-way dispute with the Denver and Rio Grande Railroad. Well paid by the Santa Fe for his services as a hired gun, Thompson returned to Austin and opened a gambling hall above the Iron Front Saloon on Congress Avenue. According to Lafayette Rogers, a local patron of the Iron Front, "Ben...never run a crooked game in his house."
Thompson's acknowledged honesty, loyalty, generosity, and prowess with a revolver impressed the citizens of Austin enough that they twice elected him city marshal. First winning office in December 1880, he proved to be an excellent officer, some claiming that he was the finest marshal that Austin had known up to that time, and was re-elected in November of the following year. In July 1882, while still serving as marshal, Thompson quarreled over a card game in a saloon in San Antonio, where he killed the prominent sportsman and owner of the Vaudeville Theatre, Jack Harris. He was indicted for the murder and resigned as marshal. After a sensational trial and acquittal, he returned to Austin to a hero's welcome and resumed his life as a professional gambler. On the evening of March 11, 1884, Thompson brashly returned to the Vaudeville Theatre with his notorious friend John King Fisher, deputy sheriff of Uvalde County. Word of their arrival in San Antonio preceded them. Within minutes of stepping into the Vaudeville the two were shot and killed from behind. Many believed that Harris's friends and partners, Joe Foster and William Simms, arranged the assassination. Thompson was survived by his wife, Catherine, and two children, Ben and Katy. He was buried in Oakwood Cemetery. Austin newspaper editors engaged those of San Antonio in a free-wheeling, nasty debate after a coroner's jury in San Antonio ruled the killing self-defense and no one was ever charged with the murders. It was Bat Masterson who later described Thompson's ability with a pistol: "It is doubtful if in his time there was another man living who equaled him in a life-and-death struggle."
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