With the rebel government in disarray during the Runaway Scrape, Independence's mission was to defend Galveston from invasion and block resupply of Santa Anna's nearby army.

[4] In the summer of 1836, Independence was the only ship of the Texas Navy on duty in the Gulf of Mexico; Liberty having been sold to pay the cost of refurbishment and Invincible and Brutus in New York City for repairs.

[4] Mexican authorities had recently repudiated the Treaty of Velasco claiming that General Santa Anna did not have the capacity to bind Mexico to recognize Texas' independence.

With rumors of an imminent invasion of Texas by Mexico, Independence carried out a screening and patrol action at Matamoros, which the Texans had ordered blockaded.

[4] When Independence sailed from New Orleans on 10 April 1837, with Texas minister to the United States, William H. Wharton aboard, she was skippered by her new Captain, George W. Wheelwright,[3] who had been left without a command after the forced sale of Liberty in May 1836.

On her next cruise, Independence had smooth sailing for about seven days when on 17 April she encountered the Mexican brigs-of-war Vencedor del Álamo and Libertador off the mouth of the Brazos River.

The final engagement took place right in front of the small Texan town and populace, including the Texas Secretary of the Navy Samuel Rhoads Fisher.

Severely wounded and taken below, command of the schooner passed to Lieutenant John W. Taylor, who finished the last few moments of battle before receiving orders from Wheelwright to surrender.