In October 1833, at the suggestion of Jeremiah Brown, Jones drifted to Texas. He had engaged passage back to New Orleans when John A. Wharton and other citizens of Brazoria urged him to "give Texas a fair trial." Jones soon had a practice at Brazoria worth $5,000 a year. As tension between Texas and Mexico mounted, he counseled forbearance and peace until the summer of 1835, when he joined in signing a petition for the calling of the Consultation, which he visited. At a mass meeting at Columbia in December 1835 he presented resolutions for calling a convention to declare independence but declined to be nominated as a delegate. When war came he enlisted in Robert J. Calder's company and during the San Jacinto campaign was judge advocate and surgeon of the Second Regiment. Nevertheless, he insisted upon remaining a private in the infantry. On the field of San Jacinto he found Juan N. Almonte's Journal and Order Book, which he sent to the New York Herald for publication in June 1836. After brief service as apothecary general of the Texas army, Jones returned to Brazoria, evicted James Collinsworth from his office with a challenge to a duel, and resumed practice.
During the First Congress of the republic, Jones became increasingly interested in public questions and critical of congressional policies. He was elected a representative to the Second Congress as an opponent of the Texas Railroad, Navigation, and Banking Company. As chairman of the Committee on Foreign Relations, he advocated a withdrawal of the Texas proposal for annexation to the United States. He was also chairman of the committee on privileges and elections and the committee on ways and means. He helped formulate legislation to regulate medical practice and advocated a uniform system of education and an endowment for a university. At the end of his congressional term, Jones planned to marry Mrs. Mary (Smith) McCrory and return to his practice at Brazoria. President Sam Houston, however, appointed him minister to the United States in June 1838 and authorized him to withdraw the annexation proposal. Jones's purpose as minister was to stimulate recognition from and trade relations with Europe in order to make the United States desire annexation or to make Texas strong enough to remain independent. Thus early he hit upon the policy of alternatives that characterized his management of foreign relations until Texas joined the Union and that gave him the title of "Architect of Annexation."
He was recalled by President Mirabeau B. Lamar in May 1839 and resolved to retire from politics, but when he arrived in Texas he found that he had been elected to finish William H. Wharton's term in the Senate. As senator he criticized the fiscal policies of the Lamar administration and the Texan Santa Fe expedition. Jones was chairman of the committees on foreign relations and the judiciary and was president pro tem of the Senate during the Fifth Congress. On May 17, 1840, Jones married Mrs. McCrory at Austin and in the spring of 1841 returned to practice in Brazoria. He declined candidacy for the vice presidency in the election of 1841, in which Houston again became president. Houston appointed Jones his secretary of state, and from December 13, 1841, until February 19, 1846, Jones managed the foreign relations of Texas through a series of crises. Both Houston and Jones later claimed to have devised the foreign policy followed by Texas after 1841, and it is impossible to determine which man originated its leading features. In the main they agreed on the purpose of getting an offer of annexation from the United States or getting an acknowledgment of Texas independence from Mexico. They preferred getting both proposals simultaneously, so that an irrevocable choice might be made between them.
Jones was elected president of Texas in September 1844 and took office on December 9. He had made no campaign speeches, had not committed himself on the subject of annexation, and did not mention the subject in his inaugural address. After James K. Polk's election as president of the United States on a platform of "re-annexation of Texas" and President John Tyler's proposal of annexation by joint resolution, Jones continued his silence. But the Texas Congress declared for joining the Union. Before Jones received official notice of the joint resolution, the charges of England and France induced him to delay action for ninety days. He promised to obtain from Mexico recognition of Texas independence and delayed calling the Texas Congress or a convention. Meanwhile, public sentiment for annexation and resentment against Jones mounted. He was burned in effigy, and threats were made to overthrow his government, but he remained silent until Charles Elliot returned from Mexico with the treaty of recognition. On June 4, 1845, Jones presented to the people of Texas the alternative of peace and independence or annexation. The Texas Congress rejected the treaty with Mexico, approved the joint resolution of annexation, and adopted resolutions censuring Jones. The Convention of 1845 considered removing Jones from office. He subsequently retained his title, though his duties were merely ministerial. On February 19, 1846, at the ceremony setting up the government of Texas as a state in the Union, Jones declared, "The Republic of Texas is no more." Then he retired to Barrington, his plantation near Washington-on-the-Brazos.
Jones hoped to be elected to the United States Senate, but Houston and Thomas Jefferson Rusk were chosen. For twelve years Jones brooded over his neglect while he became a prosperous planter and accumulated a vast estate. After an injury that disabled his left arm in 1849, he became increasingly moody and introspective, and his dislike for Houston turned into hatred. While in this frame of mind, he edited his Republic of Texas, which contained a brief autobiography, portions of his diaries, and annotated selections from his letters. The book was published in New York in 1859, after his death.
On March 1, 1835, with four other persons, Jones had established the first Masonic lodge in Texas, originally Holland Lodge No. 36 at Brazoria. He was its first head. He called the convention that organized the Grand Lodge of Texas on December 20, 1837, and was elected first grand master. He was a charter member and vice president of the Philosophical Society of Texas in 1837 and in 1853 helped found the Medical Association of Texas. In 1857 Jones believed that the legislature would send him to Washington as senator, but he received no votes. He committed suicide at Houston on January 9, 1858, and was buried in Glenwood Cemetery at Houston. The Texas Centennial Commission erected a statue of him in Anson, Jones County, both of which were named after him. Barrington, his plantation home, is preserved in Washington-on-the-Brazos State Historic Site as part of the Barrington Living History Farm.
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