Steptoe hastily ordered Mowry to leave Utah and lead a detachment of soldiers southwest through the Great Basin to Fort Tejon, California, a difficult journey across 750 miles of desert and mountains.

While at Fort Yuma, Mowry became interested in the potential mining opportunities in the land acquired from Mexico as part of the Gadsden Purchase.

[6] After leaving the Army Mowry traveled regularly between the East Coast and Arizona, involving himself in politics and mining deals.

While in Tubac on July 8, 1859, he fought a duel with Edward E. Cross, an editor for the Weekly Arizonian who had questioned the viability of an Arizona state and called the territory worthless.

[1][7] In 1860 Mowry resigned his position as delegate and accepted an appointment to serve as a Commissioner for the United States to establish an eastern boundary for California.

With the backing of wealthy investors from Rhode Island, Mowry pursued various opportunities until April 1860 when he successfully acquired the Patagonia silver and lead mine just southeast of the Santa Rita Mountains in southern Arizona.

[9] In July 1861, soon after the start of the Civil War, American forts in southern Arizona were evacuated as Union troops redeployed to fight the Confederates.

He was accused of treason for selling ammunition to rebel forces and sharing military information in letters to various Confederate officials including Jefferson Davis, Brigadier General Henry Hopkins Sibley and Captain Sherod Hunter.

[5] After release, Mowry returned to his mine to find it had been shut down because the operator lacked sufficient funds to pay wages.

For the remainder of the war, Mowry traveled between Arizona, San Francisco and New York in a tangled effort to run the mine, raise capital from investors, and seek redress from the government for perceived wrongs.

Many of Mowry's statements were contradictory, telling potential investors that the mine was still a lucrative ongoing venture but then complaining that government intervention had cost him dearly.

In particular, Mowry was bitterly angry with Carleton, claiming that his arrest was result of a grudge that the general held against him for some past incident.

Finally in November 1864 Mowry sold his mine to a group of San Francisco investors and returned to Arizona to operate it on their behalf.

[5] After leaving Arizona Mowry spent most of his time in New York City where he was involved in various speculative deals in the mining industry.

By the end of the year Lillie went on to marry B.H.Coit and when she died a bequest she left to San Francisco was used by the city to build Coit Tower.

However, public opinion had soured on him by 1870 when one Arizona newspaper commented, "He quit the Territory having sustained his reputation as an egotist, braggart and shameless liar.

"[8] Obituaries written shortly after his death noted his contributions to Arizona but also criticized him for his failure to support the Union during the Civil War.