Doheny was a major in the District Guards, a ceremonial military unit based in the U.S.M.'s Capital District, when General Herbert Williamhouse of the Confederation of North America took Tampico, Durango on July 8, 1846 and began advancing up the Tampico Road towards Mexico City. Mexican President Pedro Hermión ordered Doheny to intercept Williamhouse with the District Guards and delay him until reinforcements could arrive. Doheny was able to defeat Williamhouse's numerically superior army at the Battle of Tampico Road, forcing him to retreat back to Tampico. Hermión promoted Doheny to general and placed him in charge of the siege of Tampico. Doheny was able to contain the North Americans in Tampico in spite of their greater numbers, until Williamhouse was forced to evacuate the city on March 5, 1848.
In March 1850 word reached Mexico City that a North American army under General David Homer had advanced across Mexico del Norte and Arizona and was preparing to enter California. Doheny left the District Guards under Colonel Andre Montez and took a newly-formed army north to cut Homer's army off from retreat. Doheny's army reached the eastern end of Williams Pass in June while Homer's army was advancing west through the pass. Homer's men engaged the California brigades under General Francisco Hernandez in the Battle of San Fernando from July 5 - 7, 1850. The battle was indecisive, with both armies withdrawing from the field; however, Homer found his way east blocked by Doheny, and he was unable to leave Williams Pass.
Governor-General Henry Gilpin dispatched the Southern Confederation militia under General FitzJohn Smithers in an attempt to relieve Homer's army. However, Smithers' orders were delayed, and he did not reach Williams Pass until mid-November 1850. Over the next five months, in the Battle of Williams Pass, the four armies fought and starved in the frozen mountain passes. The Mexicans lost 66,000 out of 97,000 men, while the North Americans lost 113,000 out of 140,000. Doheny himself died of the cold in the course of the battle.
Sobel's source for Michael Doheny's role in the Rocky Mountain War is Edgar Almond's Michael Doheny: The War Years (Mexico City, 1969).