During the
American Civil War, Humphreys was critical of Indiana's
Republican governor,
Oliver P. Morton, and
President Abraham Lincoln's conduct of the war.
Harrison H. Dodd, "grand commander" of the
Sons of Liberty in Indiana, chose Humphreys as one of his major generals in a secret society who opposed the war. On September 17, 1864,
General Alvin Peterson Hovey, commander of the Military District of Indiana, authorized a military commission to meet on September 19 at
Indianapolis, Indiana, to begin trials of Dodd and others placed under military arrest. On October 7, 1864, Humphreys was arrested and imprisoned in the Federal Building at Indianapolis, where he became one of the defendants in the Indianapolis treason trials before the military commission. Among the other men accused of treason were Democrats
Lambdin P. Milligan, a lawyer living in
Huntington, Indiana;
William A. Bowles of
French Lick, Indiana; and Stephen Horsey of
Martin County, Indiana. The military commission for the trial of Humphreys, Milligan, Horsey, and Bowles 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." The 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 and Illinois; and make war on the U.S. government. Democrats charged that the arrests and trials by military commission were politically motivated amid a climate of bitter political disputes between Democrats and Republicans about the conduct of the war. Scholars who studied the trials, which were highly publicized in the press, 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. The controversial proceedings led to the landmark U.S. Supreme Court case known as
Ex parte Milligan. The Court ruled the application of
military tribunals to citizens when civilian courts are still operating is unconstitutional. On December 10, 1864, the commission found Humphreys, Milligan, Horsey, and Bowles guilty on all charges. Humphreys was sentenced to hard labor for the remainder of the war. Compared to the others accused as co-conspirators, the case against Humphreys was weaker and his sentence was less severe. (Milligan, Bowles, and Horsey were sentenced to hang, but the sentences were commuted to life imprisonment in May, 1865.) Three weeks after his conviction, and with President Lincoln's support, General Hovey modified Humphreys's sentence, allowing his release. Humphreys was required to remain within two specific townships in Greene County and could not participate in any acts that opposed the war. After the
U.S. Supreme Court handed down their ruling in
Ex parte Milligan on April 3, 1866, the men were released from custody. ==Later career==