In a court case that was to have long-reaching effects even to the 21st century, Lambdin P. Milligan and William Bowles, condemned to be executed in the first week of June, were reprieved and sentenced to life imprisonment. Proceedings had been instituted in Federal court to reverse their conviction by military court-martial on charges of conspiring against the United States, giving aid and comfort to the Confederacy, and inciting insurrection. Milligan was a prominent leader of the Copperheads in Indiana; he had been arrested on Oct. 5, 1864. On Dec. 17, 1866, the U.S. Supreme Court in ex parte Milligan unanimously ruled that Milligan be released from prison. A majority of the court ruled that neither the President nor the Congress had the power to order military commissions to try civilians outside the actual theatre of war. A minority believed that the Congress had the power. During the trial by a military commission of the conspirators in the assassination of Abraham Lincoln, then still going on in Washington in June 1865, defense attorneys tried unsuccessfully to get the military commission ruled invalid, inasmuch as the eight defendants were all civilians, and the district courts were open and functioning in Washington at the time.
On Tuesday, June 6, the citizens of Missouri ratified a new state constitution which include the abolition of slavery. The Confederate guerrilla fighter William Quantrell died in Louisville the same day, of wounds he had received on May 10.
President Andrew Johnson ordered that Confederate prisoners of war who were willing to take the Oath of Allegiance to the United States were declared released. Officers above the rank of Army captain or Navy lieutenant were not included. In Washington, the Sixth Army Corps of the Army of the Potomac, which had missed participating in the Grand Review in Washington on May 23, held its own parade in Washington on June 8. The following day, another serious ammunition explosion occurred in Chattanooga. An ordnance building blew up after it had been set afire by sparks from the funnel of a locomotive standing on a nearby siding. Ten people were casualties and the building was destroyed.
In an effort to restore pro-Union governments in six of the southern states before the Republicans in the Congress could intervene, President Johnson went about the first and second week of June appointing provisional governors; he also restored to the Union his home state of Tennessee, since it had reorganized its own government (Johnson had been military governor when he had been asked to serve on the ballot as vice president by Abraham Lincoln in 1864). On the high seas of the Pacific Ocean, CSS Shenandoah was still busy stopping and taking U.S. commerce vessels and whaling ships. As the second week of June closed, there was one organized body of Confederate troops still operating in the field. Commanded by Brigadier General Stand Watie, a full-blooded Cherokee, his Indian Brigade was still fighting small skirmishes and engagements with Union troops in the Indian Territory (now Oklahoma).