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Both Stephen F. Austin and Henry Smith wanted to be the republic's first president, but many Texans supported Sam Houston, The Hero of The Battle of San Jacinto for office. Less than two weeks before the election, Houston was finally convinced to run and won easily, and Mirabeau Lamar, another hero of the revolution, became vice president, and Houston brought his defeated presidential rivals into the government, Smith as secretary of the treasury, and Austin as secretary of state, though soon after, he died, and the new nation faced many issues and challenges, as it had no money and was greatly in debt, had no other countries to recognize its independence, and the Comanche and Kiowa remained in control of western Texas and continued to carry out raids on settlements.

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The Waco, Comanche, Kiowa, and other Native American groups resented the Texans living on lands they viewed as their own, and even the Cherokee leader Chief Bowles, who was Houston's friend, threatened to join the Mexicans against Texas if war broke out again. While Sims was negotiating peace with some Native Americans, other groups were getting ready for war, and in the 1820s, the Cherokee had moved into East Texas, and they were angry because after the revolution many Americans had settled on land claimed by Native Americans.

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The Constitution of 1836 stated that the president could not serve consecutive terms, meaning that Houston couldn't seek reelection after his term expired in 1838, so Houston began to search for a candidate who would continue his policies. A little known senator, Robert Wilson, finally agreed to run, but Mirabeau Lamar had already decided to run for president, and as vice president, had opposed many of Houston's policies, and his campaign focused on the failure of Houston's peace policy to end Indian attacks, and also criticized Houston's inability to gain recognition of Texas' independence in Europe or by Mexico, and Lamar won easily, and Lamar's goals for Texas were different than Houston's, as he opposed annexation of Texas by the United States because he thought Texas could become a powerful nation, to do this he first expanded the Texas Rangers and rebuilt the navy to end the threat posed by Mexico and the Native Americans, and by 1839, France was convinced the U.S. would not annex Texas, and Britain and the Netherlands did so too a year later.

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January, 1839-Texas sets land aside for schools

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January, 1839-Texas sets land aside for schools

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Improving education was another one of Lamar's goals, and like Thomas Jefferson, Lamar believed that a republic's citizens must be well educated so they can make intelligent decisions about voting and other civic duties, and Congress responded by setting nearly 18,000 acres of land aside in each public county for the support of public schools. Schools were eventually built on this land, and the rest was sold over time to pay for the costs of operating the existing schools, and land was also reserved by Congress for two universities, and it would be many years before Texas A&M University and the University of Texas would be opened, and churches operated the first colleges in Texas, and Baylor University, first founded in 1845 by Baptists, is the oldest university in Texas.

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Lamar distributed the Cherokee and believed they had no legal claim to their Texas lands, and Lamar convinced the Congress to reject the treaty Houston had negotiated with the Cherokee in 1836, and the involvement of some Cherokee in the 1838 Cordova Rebellion caused Lamar, like some other Texans, to believe that the Cherokee were allied with Mexico. In May, 1839, Texas Rangers killed several Mexicans and Native Americans who were carrying out raids in Texas, and on the body of the raid's leader, documents were found that seemed to link the Cherokee to a Mexican plot to reconquer Texas, and when Chief Bowles denied this, Lamar still ordered the Cherokee out of Texas, and the Cherokee agreed to leave after they harvested their crops, but Lamar would not wait, and ordered the Texas army to remove the Cherokee by force, and and on July 16, 1839, the Texas army attacked the Cherokee near the Neches river and several Texans were killed, as well as 100 Cherokee, including Chief Bowles, and for a week, the Texas army burned Cherokee villages, farms, and crops, and the remaining Cherokee were forced out of their land, fleeing across the Red river and out of Texas.

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January, 1840-Lamar sends navy to Mexico

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January, 1840-Lamar sends navy to Mexico

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Lamar thought that having a strong military would force Mexico to recognize Texas independence, and a newly formed Texas navy obtained eight vessels to replace the ones lost during and after the revolution, and Edwin W. Moore, a 29-year old U.S. Navy officer, came to Texas to command the Texas Navy and was assigned the rank of commodore. In 1840 Lamar ordered the Texas Navy to aid Mexican rebels in Mexico's Yucatan province, and the rebels agreed to pay Texas for the Navy's aid, and Lamar believed that the Yucatan Rebellion would keep Mexico's military occupied and prevent further attacks on Texas, Lamar also hoped that in turn for ending the aid, Mexico would recognize Texas, and when the talks with Mexico failed, Moore helped protect the Yucatan rebels by defeating and capturing a number of Mexican ships.

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In West Texas, the Comanche raided settlements and the Texas Rangers entered the area in 1839 and fought many battles, until the Comanche sought to end the fighting in early 1840 by asking for a peace treaty, and the Texas leaders agreed to meet and discuss a treaty if the Comanche chiefs brought all of their white captives with them, and when the meeting took place in San Antonio's Council House on March 19, 1840, only one white captive was brought that told the Texans the Comanche still had other captives, and the Texas Rangers tried to hold the Comanche negotiators hostage until the other captives were returned. A struggle, known as the "Council House Fight" broke out in which 7 Texans and 35 Comanche were killed, and to avenge the deaths of their negotiators, the Comanche killed most of their captives, and in 1840, about 500 Comanche swept down the Guadalupe River to attack Victoria and Linnville, and as the Comanche moved back west, a force of about 200 Texan volunteers pursued them, and about 2 battles were fought, and the Comanche retreated north of the Red River, and in 1841, Lamar ordered similar attacks on Wichita towns in North Texas, and the next year the Wichita asked for peace, and the Native Americans suffered greatly from Lamar's policies but greatly decreased the number of raids, although they still occurred during and after his term of office.

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Relations between Mexico and Texas grew worse in 1841 due to Lamar trying to annex Santa Fe to the republic, and Santa Fe was in an area of land that both Texas and Mexico claimed, and Lamar saw control of New Mexico as the first step to the republic's expansion to the Pacific Ocean. When the Congress didn't approve of Lamar's plan to conquer New Mexico, he did it anyway, and in June of 1841, José Antonio Navarro with over 300 soldiers and merchants to invite Santa Fe to join the republic, heat, shortages of food and of water, and attacks by Native Americans all plagued the expedition and as they neared their destination, Mexican troops stopped them and forced them to surrender, and the Texans were marched to prison in Mexico City, and many died along the way, and the survivors were freed in April of 1842 due to the efforts of British and U.S. diplomats.

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Lamar's policies proved very costly, in terms of money and in loss of life, as the wars against the Native Americans cost the Republic nearly $2.5 million. Lamar had also failed in his attempts to borrow money from the U.S. and European nations, and the government had issued paper money known as redbacks, but they quickly lost value, and by the end of Lamar's term were only worth 2 cents in some parts of Texas, and became illegal to use to pay taxes due to them becoming so worthless, and Republic's public debts had rose to $8 million.

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In September of 1841, the Texas voters returned Houston to presidency, and he easily defeated Lamar's chosen successor, Vice President David Burnet, after a bitter campaign, and in his first message to Congress, he stated that he would undo all of the damage he felt was done to the Republic by Lamar's policies. Houston's plans focused on cutting the costs of the government, making peace with Native Americans, and pursuing annexation by the United States.

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In March, 1842, about 700 Mexican soldiers invaded Texas and captured San Antonio, and soon withdrew to Mexico, but Houston ordered the government's archives to be moved from the city of Austin, in case it were to be attacked. Austin's citizens suspected that Houston planned to move the capital and when the Texas Rangers arrived to move the archives, some residents fired at them, but the Rangers didn't fire back to avoid bloodshed, and the event, known as the "Archive War", ended with the capital and archives staying in Austin, and when about 1,500 Mexican troops seized San Antonio again, Texas volunteers and a small band of Texas Rangers led by Jack Coffee Hays were prepared and defeated the Mexican army just east of the city at the Battle of Salado Creek.

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October, 1844-Houston meets with Native tribes

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October, 1844-Houston meets with Native tribes

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Houston renewed peaceful and fair dealings with the Native Americans, as well as establishing trading posts to provide them with supplies, and sent agents to try and convince the Native Americans that Texas wanted peace, and peace treaties and trade agreements were signed with several Native American groups. Houston also met with the leaders of the Comanche and ten other groups and explained how Lamar's policies had ended, and eventually 11 other Native groups signed the peace treaties that resulted from the talks.

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Anson Jones, who, in 1844, was elected president of Texas, called a special session of the Congress to consider both annexation offers, from the U.S., and from Mexico. The congress quickly accepted annexation and the delegates chosen by voters at a special convention agreed, and members of the convention then wrote a new state constitution.

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During the republic, Texas' population grew at about 7,000 people a year, and the main source of this was immigrants, the U.S. being the main source of the immigrants, and the new American arrivals had generally favored annexation, and when Houston took office for his second term as president, he still favored annexation and he had a more willing partner than before, John Tyler, who also favored annexation and proposed the idea to Houston. In April of 1844, representatives sent from the United States and Texas negotiated and signed a treaty of annexation stating that Texas would join the U.S. as a territory and the U.S. government would pay off all of the republic's debt and in turn, Texas would give up all of its claims to public lands, and some Texans were disappointed with the treaty terms and argued that Texas should keep its public land claims, as land sales were a good and important source of revenue, and others were upset that Texas would enter only as a territory and not a state, but most Texans favored the treaty terms and were confident the U.S. would accept them.