Appointed secretary of war of the Republic of Texas, he served from December 21, 1836, to November 13, 1837, but his was a recess appointment and was not confirmed when the Senate met because of the change to the Mirabeau B. Lamar administration. On January 23, 1837, Lamar appointed Fisher lieutenant colonel of a frontier cavalry regiment. On March 19, 1840, he was in command of two companies of regulars at San Antonio at the time of the Council House Fight. Later in 1840 he was attracted to the Republic of the Rio Grande and led 200 men to join the army of that organization at San Patricio.
Returning to Texas after a few months of unsuccessful campaigning, he joined the Somervell expedition in 1842 and was elected captain. With Alexander Somervell's abandonment of the enterprise, Fisher was elected leader of those members of the expedition who continued on into Mexico on the Mier expedition. During the attack on Mier, Fisher was wounded. Imprisoned with his men by the Mexican general Pedro de Ampudia, Fisher was marched to Perote Prison. He was released in 1843 and returned to Texas, where he died at his home in Jackson County in 1845.
29° 17.617, -094° 48.701
Trinity Episcopal Cemetery