Governor Richard Yates commissioned the raising of the company, and Morgan was elected its captain, in which capacity he served until the close of the war, when he received an honorable discharge on June 26, 1865.

While in the service he was for two years provost marshal, stationed at Clarksville, Tennessee, where he had charge of all the abandoned and contraband goods, houses and lands of all persons who had joined the rebel army in that vicinity.

[3] Morgan was nominated by President Rutherford B. Hayes as Chief Justice of the Idaho Territorial Supreme Court on May 19, 1879, and was confirmed by the senate on June 10, 1879.

[4][5] Morgan's four-year term expired on June 10, 1883, but as is typical for Article I judges, he continued serving, and he was renominated by President Chester A. Arthur on July 3, 1884, and was confirmed by the senate two days later.

[1] Morgan died in his home in Boise, following a paralytic stroke,[9] and was memorialized in the reports of the Idaho Supreme Court the following year.