When Houston took office again, the Texas economy was very bad. The treasury was empty, inflation was high, and the Texas paper currency was almost worthless. Houston cut down the number of government offices and salaries. He believed that annexation to the United States would help.
Santa Anna returned to power in Mexico. He sent forces north into Texas, capturing a few cities for a few days. He wanted to push Texas into invading Mexico, in which case Mexico would crush the Texans. Houston knew that Texas could not survive another war, so he made peace offers to Mexico. Santa Anna replied by sending a second invasion.
Houston sent a force of 700 volunteers to the border. The eager men decided to continue into Mexico, crossing the Rio Grande at Mier. After a fierce battle, the Texans were forced to surrender. Many of the prisoners escaped, but 176 were recaptured. Santa Anna executed every tenth man, a disastrous ending to what became known as the Mier Expedition.
Houston feared Mexico might recapture Austin, so he wanted to move the capital. He ordered the removal of all government papers from Austin. The people of Austin wanted to keep the capital, so they chased down Houston's men, bringing the papers back to Austin at gunpoint and hiding them. This was an embarrassing incident for the president. For the remainder of his term, he conducted governmental affairs from Washington-on-the-Brazos.
In the final year of Houston's second presidency, the annexation fight returned. Houston acted behind-the-scenes with the United States, England, France, and Mexico. He seemed to deliberately encourage another war with Mexico, building U.S. fears that Texas might be lost forever without a quick annexation.
The U.S. administration negotiated a treaty of annexation with Texas and sent it to the Senate for approval. Instead, it was overwhelmingly defeated due to party politics, anti-slavery views, and fears of war with Mexico.
Texas annexation became the major issue in the 1844 U.S. presidential campaign. Sam Houston knew that his term of office would end before any decision was made. Determined to leave Texas with a successor who could lead Texas through the annexation process, he chose Anson Jones, his secretary of state, to follow him as Texas president.
Source: Sam Houston (Second Term)
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