Shortly after his arrival, Wharton was embroiled with the Austin family in a feud that eventually led to a duel between him and William T. Austin. Wharton was shot in the right wrist and never fully regained the use of his hand. Around the same time, he participated in the establishment of the first Masonic lodge in Texas. Wharton was an early activist in the movement for Texas independence. He attended the assembly in Columbia that preceded the Consultation and was appointed to the Committee of Vigilance, Correspondence, and Safety of the Department of Brazoria. As a member of this committee, Wharton corresponded with political leaders throughout Texas to consolidate opposition to the Centralist government in Mexico City. At the Consultation in San Felipe in the fall of 1835, he advocated immediate independence from Mexico and was appointed chairman of the committee to list grievances and explain the call to arms. He later served as a member of the General Council of the provisional government.
On December 8, 1835, Sam Houston appointed Wharton Texas agent to New Orleans to procure supplies for the army. Wharton also served as adjutant general on Houston's staff and was responsible for bringing the Twin Sisters to the army. Secretary of War Thomas J. Rusk later recognized Wharton for bravery during the battle of San Jacinto. After the Texas Revolution Wharton attempted to gain the release of his brother and other Texans captured on the naval vessel Independence and imprisoned in Matamoros. Upon his arrival in Mexico, however, he too was imprisoned. The brothers soon escaped and returned to Texas.
John served briefly as the secretary of war until October 1836, when he left the position to become a representative from Brazoria in the First Congress of the republic. He returned to Houston after completion of his term in office and for two years practiced law with Elisha M. Pease and John Woods Harris. Wharton left the partnership to serve in the Third Congress. During this term in the House he acted as chairman of the committee on education but fell ill with fever and had to leave the position. He died on December 17, 1838, and was buried with military and Masonic rites. David G. Burnet, who delivered the funeral oration, described Wharton as "the keenest blade of San Jacinto."
29° 45.453, -095° 22.753
Founders Memorial Park