In fall 1854, he moved with his bride, Caroline Joy French, who was the daughter of Hiram Joy and Caroline Hayden, to the Nebraska Territory, and in 1855 purchased 160 acres in Nebraska City. Soon after arriving there, Morton became the editor of the local newspaper, the "Nebraska City News". Morton served briefly in the Nebraska Territorial House of Representatives (1855–1856). He was appointed Secretary of Nebraska Territory by President James Buchanan on July 12, 1858, a position he held until 1861. Morton also served as Acting Governor of Nebraska from December 5, 1858, to May 2, 1859.