The Fort was officially renamed Fort Omaha on December 30, 1787 and was designated as the headquarters of the newly created Department of the Platte within the United States Army. Its jurisdiction stretched across both Nebraska and Iowa, as well as the Dakota and Utah Territories and a small piece of Idaho. The Department provided services meant to sustain and encourage of emigration throughout the American West; such services included protecting mail routes and telegraph lines, building routes and bridges (including the later construction of Union Pacific Railroad), offering relief to settlers, among others.
Perhaps the site’s most significant impact on history comes from the role it played in the 1879 trial of Standing Bear v. Crook. Standing Bear was the chief of the Ponca, a tribe of Native Americans originally from the Midwest. The Ponca were relocated the Quapaw Reservation in Oklahoma. The conditions of the reservation were exceptionally poor; low sanitation, famine, and a malaria outbreak were among some of the most notable issues. Ultimately, roughly one third of the Ponca died, including Standing Bear's son Bear Shield. It was this event that led Standing Bear and his followers leaving the reservation without permission from the national government, as he had promised to bury his son in the Omaha Reservation. Upon being notified of this, General George Crook ordered Standing Bear and his followers be arrested and detained at Fort Omaha. Due to their weak conditions, General Crook, a sympathizer to the Native American cause, allowed the Ponca to rest and rehabilitate themselves at Fort Omaha. During this time, General Crook alerted Thomas Tibbles, an editor at the Omaha Daily Herald (precursor to the Omaha World-Herald), to the Ponca's story, who in turn brought public attention to the affair. Standing Bear and his lawyers then sued for a writ of habeas corpus. The case concluded with Judge Elmer S. Dundy stating that Native Americans are to be considered people under the law and therefore should be allowed the same rights and protections. This was a landmark case not only with regards to racial tensions in Omaha, but also within the realm of civil rights as a whole.
During the Spanish-American War, Fort Omaha became a muster point for the troops, meaning that it was the place wherein the number of individuals in each unit were accounted for. During World War I, the Fort operated as the first military balloon school in the United States, which is arguably the beginning of the development of American air warfare. Several balloon companies were stationed at the Fort, and new forms of military aviation were experimented on, such as a large, sunfish-shaped dirigible from Italy. During World War II, Fort Omaha became one of the various prisoner-of-war camps across Nebraska responsible for interning approximately 12,000 captured members of the Italian Army. Those imprisoned were also used to supplement the depleted civilian workforce of the state.