Hamilton's political career began in 1849, when Gov. Peter H. Bell appointed him acting attorney general. He also represented Travis County for a single term (1851-53) in the state House of Representatives. By the 1850s he had become a member of the "Opposition Clique" in Texas, a faction of the regular Democratic party that opposed secession, reopening the slave trade, and other Southern extremist demands. As such, in 1859 Hamilton won election to the United States Congress from the Western District of Texas. He served on the House committee formed during the secession winter of 1860-61 to try to solve the sectional crisis. When he returned to Texas in the spring of 1861 he won a special election to the state Senate, and he remained in Austin until July 1862, when alleged plots against his life forced him to flee to Mexico.
Hamilton became a hero in the North and delivered speeches in New York, Boston, and other Northern cities. His rhetorical targets included slavery, disunionists, and the "slave power," which he believed was trying to subvert democracy and the rights of non-slaveowners. After he met with President Abraham Lincoln in November 1862, he accepted a commission as brigadier general of volunteers and an appointment as military governor of Texas. Hamilton accompanied an unsuccessful federal expedition into South Texas in late 1863 and spent most of the rest of the war in New Orleans, where his family joined him late in 1864.
His career during Reconstruction was stormy and frustrating. As provisional governor from the summer of 1865 to the summer of 1866, he pursued a program of trying to limit officeholders to former Unionists, ratifying the Thirteenth Amendment to the United States Constitution, and granting economic and legal rights (although not the vote) to freedmen. When the Constitutional Convention of 1866 refused to enact most of Hamilton's suggestions, he rejected presidential Reconstruction and promoted the harsher program of the Radical Republicans. He endorsed black suffrage and helped organize the Southern Loyalists' Convention in Philadelphia in September 1866. For a time he served as a bankruptcy judge in New Orleans, but in 1867 he returned to Texas as an associate justice on the state Supreme Court.
Hamilton played a leading role in the Texas Constitutional Convention of 1868–69 and served on the Republican National Executive Committee. His political views changed again, however; he once again came to favor a quick reconstruction of Texas. He opposed the Radicals' scheme for turning West Texas into a separate, Unionist state and withdrew his support for black suffrage. As a result, although his brother Morgan C. Hamilton was a leading Radical spokesman and United States senator, Hamilton became one of the state's leading moderate Republicans and ran against Radical Edmund J. Davis in the 1869 governor's race. Davis won, but Hamilton remained a vocal opponent of Radical policies. Hamilton never sought public office after this defeat. In 1871 he was a leader in the Tax-Payers' Convention. He practiced law and worked on his farm near Austin. He died of tuberculosis on April 11, 1875, and was buried in Oakwood Cemetery, Austin.
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