On February 11, Neill left the Alamo, to care for his family, overcome with a serious illness. He transitioned command to William Barret Travis, the highest-ranking regular army officer in the garrison. Due to a rift in the command of the Alamo between Bowie and Travis, Neill returned to the Alamo on February 14 and settled the dispute. A resolution was reached; Bowie and Travis would hold joint command of the Alamo. Neill would leave San Antonio just before the siege of the Alamo. On the day of the final Alamo battle, Neill was in Gonzales steadily working to increase the roster of the Alamo relief forces. In Gonzales, he signed a personal voucher on March 6, for ninety dollars to buy medicine for the Alamo garrison. Neill was intent on heading back to the Alamo where unknown to him, the fort had already fallen to Mexican troops on March 6, during the Battle of the Alamo. On March 7, Neill with Burleson gathered 50 men and headed for the Alamo.