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Polk administration, 1845–1849

After the 1844 election, Clay returned to his career as an attorney. Though he was no longer a member of Congress, he remained closely interested in national politics. In 1846, the Mexican–American War broke out after American and Mexican forces clashed at the disputed border region between Mexico and Texas. Initially, Clay did not publicly oppose the war, but privately he saw it as an immoral war that risked producing "some military chieftain who will conquer us all." He suffered a personal blow in 1847 when his son, Henry Clay Jr., died at the Battle of Buena Vista. In November 1847, Clay re-emerged on the political scene with a speech that was harshly critical of the Mexican–American War and President Polk. He attacked Polk for fomenting the conflict with Mexico and urged the rejection of any treaty that added new slave territory to the United States. Months after the speech, the Senate ratified the Treaty of Guadalupe Hidalgo, in which Mexico ceded hundreds of thousands of square miles of territory known as the Mexican Cession.

By 1847, General Zachary Taylor, who commanded the American forces at Buena Vista, had emerged as a contender for the Whig nomination in the 1848 presidential election. Despite Taylor's largely unknown political views, many Whigs believed he was the party's strongest possible candidate due to his martial accomplishments in the Mexican–American War. One of Clay's most trusted allies and advisers, John J. Crittenden, was Taylor's de facto campaign manager. Clay had initially told his allies that he would not run in the 1848 presidential election, but he was unwilling to support Taylor, a "mere military man." On April 10, 1848, he announced his candidacy for the Whig nomination. Although Webster and Winfield Scott each commanded a limited base of support in the party, Taylor and Clay each saw the other as their lone serious rival for the Whig nomination. As Taylor commanded the support of most Southern Whigs, Clay focused his efforts on courting Northern Whigs, emphasizing his opposition to the Mexican–American War and his life-long support for the gradual emancipation of slaves in Kentucky. Clay presented a strong challenge to Taylor at the 1848 Whig National Convention, but Taylor won the presidential nomination on the fourth ballot. Partially in an attempt to please the Clay wing of the party, the convention nominated Millard Fillmore as Taylor's running mate. Clay was embittered by his failure at the convention, and he did not campaign on behalf of Taylor. Nonetheless, Taylor won the election, taking 47.3 percent of the popular vote and 163 of 290 electoral votes.