In 1863 Harrison H. Dodd, leader of the Order of Sons of Liberty (OSL) in Indiana, named Bowles a major general for one of four military districts in the state's secret society that opposed the war.

Following his release from prison in 1866, Bowles returned to Orange County, Indiana, where his failing health continued to decline in the years prior to his death.

Bowles was a co-defendant in a controversial trial by a military commission that convened on October 21, 1864, at Indianapolis, that led to the U.S. Supreme Court decision in 1866 in what became known as Ex parte Milligan.

[citation needed] After it was determined that the mineral springs were not saline enough to make it practical for state-sponsored salt mining at French Lick, the acreage was sold at public action.

In 1832 the Bowles brothers bought lands totaling almost 1,500 acres that included the salt springs at French Lick from the state government.

[citation needed] As a young man, Bowles became a minister in the Baptist church in what is now known as West Baden, Indiana, but he was expelled after quarreling with its members.

[7] In 1846 Bowles was one of several men who helped organize a local militia company to fight in the Mexican–American War, the result of federal legislation such as the Wilmot Proviso.

[14] However, a court of inquiry considered accusations made against Bowles for "incompetency," ignorance of proper military tactics, "misbehavior," and cowardice.

The court cleared Bowles of the charges of cowardice as the regimental leader, but military reports found he did "manifest want of capacity and judgment as its commander.

"[15][16] After the completion of his military service, Bowles returned to Paoli, and the management of the hotel he had built at French Lick, but not without challenges and successes.

[19] Bowles, a talkative and outspoken advocate of slavery as an institution, was a peace Democrat who was sympathetic to the southern cause during the American Civil War.

[20] On February 15, 1861, at a public gathering in French Lick, Bowles was one of several local citizens who introduced resolutions in opposition to war with the South.

[21] During the 1850s and early 1860s Bowles organized local groups and recruited membership in the Knights of the Golden Circle (KGC), a secret society that supported the southern cause within the region.

[22] In 1863 Harrison H. Dodd, "grand commander" of the Order of Sons of Liberty (OSL) in Indiana, named Bowles a major general for one of the four military districts in the secret society that opposed the war.

[31] The military commission for the trial of Bowles, Milligan, Horsey, and Humphreys convened at Indianapolis on October 21, 1864, to consider five charges against the men: conspiracy against the U.S. government; offering aid and comfort to the Confederates; inciting insurrections; "disloyal practices"; and "violation of the laws of war.

"[32][33] Bowles and his co-defendants were alleged to have established a secret organization that planned to liberate Confederates from Union prisoner-of-war camps in Illinois, Indiana, and Ohio; seize an arsenal to provide the freed prisoners with arms; raise an armed force to incite a general insurrection; join with the Confederates to invade Indiana, Illinois, and Kentucky; and make war on the U.S.

Scholars who have studied the trials have proposed that they were prompted by partisan politics, convened before commission of biased military officers, failed to follow the rules of evidence, and used questionable informers as witnesses.

[33][36] The sentence for Humphreys was soon modified, allowing his release, but he was required to remain within two specific townships in Greene County, Indiana, and could not participate in any acts that opposed the war.

Efforts were made to secure pardons for Bowles, Milligan, and Horsey, with the decision passing to President Andrew Johnson following Abraham Lincoln's assassination.

Two judges, David Davis and Thomas Drummond, disagreed over the issue of whether the U.S. Constitution prohibited civilians from being tried by a military commission and passed the case to the U.S. Supreme Court, where it became known as Ex parte Milligan.

[40] The Court's ruling decreed that a writ of habeas corpus could be issued based on the congressional act of March 3, 1863; the military commission had no jurisdiction to try and sentence the men; and the accused were entitled to discharge.

Under the U.S. Constitution, the accused had a right when charged with a crime, to be tried and punished according to the law, including security against unreasonable search and seizure, a warrant for probable cause before arrest, and if indicted, a speedy trial by jury.