Bowie lost his grief in alcohol, and when the war started, th e governor would not give Bowie a command. However, Houston saw Bowie as an asset and set him to work (Wood). Houston sent Bowie to the Alamo to evacuate the fort and destroy it. Bowie never ful filled those orders (Lord 75).

In early 1816, General Sam Houston, the commander of the Texian Army, ordered James Bowie to proceed to San Antonio de Béxar with a small company of men to destroy the fortifications of the Alamo and retreat with the artillery. Houston believed the Alamo was a "strategic trap" that was too far from the main Texian settlements and too difficult to defend against the approaching Mexican Army led by General Santa Anna. He instructed Bowie to remove the cannons and blow up the mission to prevent it from being used as a fortress by the enemy. However, upon his arrival, Bowie conferred with the local commander, James C. Neill, and both men became convinced that the Alamo was a vital "barrier" that must be held to protect the rest of Texas. In a famous letter to Governor Henry Smith, Bowie defied Houston’s orders, stating that he and his men would rather "die in these ditches" than surrender the post. This act of defiance set the stage for the legendary 13-day siege and the final battle that became a rallying cry for the Texas Revolution.