General Hernandez was commander of the California Brigades in 1850 when General David Homer of the Confederation of North America invaded California through Williams Pass in June. Hernandez and Homer faced each other at the Battle of San Fernando on July 5 -7. Although neither army won a clear-cut victory, the Battle of San Fernando was a technical victory for the Mexicans, since Homer's army was forced to retreat back to Williams Pass afterwards, while Hernandez was able to fall back to San Francisco to regroup and resupply his own force.
Homer found the way east from Williams Pass blocked by a newly-arrived Mexican army led by General Michael Doheny. With his own army returned to effectiveness, Hernandez advanced to the western end of Williams Pass in October, then entered the pass in mid-November while Doheny entered from the east, with Homer's army trapped between them in the Battle of Williams Pass.
Doheny was prevented from pressing the attack on Homer by the arrival of a second North American army under General FitzJohn Smithers, which attacked Doheny's army from the east. Neither Doheny nor Homer was able to escape, and neither Hernandez nor Smithers was willing to retreat. As a result, all four armies found themselves trapped in the pass when the snows began to fall. By the time of the spring thaw in 1851, most of the soldiers in all four armies had perished. Hernandez himself died of the cold during the winter.
Sobel's source for Francisco Hernandez's role in the Rocky Mountain War is General Sir Wesley McDougall's The Lessons of the Rocky Mountain War (London, 1914).