He moved to Denver, then in the western part of the Territory of Kansas, in 1860 and continued to practice law, becoming one of the city's more distinguished lawyers.

In 1862, a Confederate army was invading the New Mexico Territory, had defeated Col. Edward R. S. Canby's troops at the Battle of Valverde, and captured Albuquerque and the capital of Santa Fe.

The Texans were pushing the Coloradans back, but the battle was turned to a victory for the Union after Slough sent Major John M. Chivington on a flank attack which destroyed the Confederate's supply train.

Slough met with Canby, determined the war in New Mexico was over, resigned his commission, and immediately headed to the Eastern theater.

At the first anniversary after the Battle of Glorieta Pass, his former Colorado troops sent him a gold inlaid sword as thanks for making the rag tag volunteers into a fighting force.

When the Civil War ended in 1865, Slough resigned his commission and opened a law office in Washington, D. C. In January 1866, United States President Andrew Johnson appointed him to serve as chief justice of the New Mexico Territorial Court.

One of his first and most personal acts was to seek funds to mark the graves of the Union dead and place monuments at the Civil War battle sites of Valverde, Apache Canyon, and Glorieta Pass, New Mexico (only one in Santa Fe was erected).

In February, 1867, he attacked the system of peonage in New Mexico in anticipation of the Federal law against debt peonage—involuntary servitude—signed by President Johnson March 2, 1867.

[3] In a mockery of a trial, Rynerson was found not guilty (by reason of self-defense), an example of the growing power of what became known as the Republican-controlled Santa Fe Ring.

The historian Richard Henry Brown says that the murder of Slough "helped affirm the position of New Mexico as 'apparently the only place where assassination became an integral part of the political system.