At this time, Moore also began to feud with his second-in-command, Commander John G. Tod, who managed the naval station at Galveston. Tod prided himself on the job he had done in supervising the construction and outfitting of the Texas ships built in Baltimore. When Moore began to point out shortcomings, such as weak anchor chains, rotten masts, awkward rigging, and other evidence of shoddy workmanship, he made an enemy of Tod.

Moore managed to persuade President Lamar to lay up only the steamship Zavala, and allow him to keep the rest of the Navy busy with a survey of the Texas coast. During his visit with Lamar, Moore also secured more than $100,000 in promissory notes and government bonds to use to pay his sailors. Since Texas had no money, the bonds were worth nothing more than an IOU, and as soon as Moore was back in Galveston he received a letter asking him to return the notes. Moore declined, replying that he had already used them to persuade the sailors to sign on for more duty. The work done by the Texas Navy that spring resulted in the first accurate navigation charts of the Gulf of Mexico. As a result, shipping losses plummeted, and insurance rates for ships going to Texas dropped, a boost to the Texas economy.

In the meantime, President Mirabeau B. Lamar and his secretary of state, Samuel A. Roberts, had become disillusioned with the prospects for peace with Santa Anna's government. Mexico had rebuffed Texas and British negotiators and was contracting to buy two steam warships, the Montezuma and the Guadaloupe. At the same time as Lamar was launching the ill-fated Santa Fe expedition (see Texas Treasures for more), he entered secret negotiations with Colonel Martin F. Pereza of Yucatán to form an alliance against Mexico. As long as Yucatán remained in rebellion, Mexico would be tied up there and unable to mount a fresh invasion of Texas.

In September 1841, Lamar and Pereza struck a deal, announced at a great ball at the Capitol in Austin. Yucatán would pay Texas $8000 a month for the services of three ships to defend its coast against Mexican raiding, and the two upstart republics would split the proceeds from any prizes seized.

The Yucatán Rebellion

General Santa Anna had retired from public life for a short time after his defeat at San Jacinto, but reemerged in 1838 to defend Mexico against a French invasion. He lost a leg in a battle at Veracruz. After the war was settled, Santa Anna consolidated his hold on the army and used it to once again make himself president of Mexico.

Several Mexican states were deeply resentful of the dictatorial methods of the central government. In May 1838, an insurrection began in Yucatán, and in 1840 the local assembly approved a declaration of independence for the state. Santa Anna's representative, Andrés Quintana Roo, negotiated a treaty to keep Yucatán in the Mexican union, but Santa Anna soon violated the treaty. In response, the Yucatecan governor ordered all Mexican flags hauled down and replaced with the flag of the new Republic of Yucatán. The assembly drafted a new constitution based on the Mexican Constitution of 1824, which had also been a rallying point for the Texas revolution.

The Yucatecans formed an alliance with Texas to fight against the Mexican naval blockade of Yucatán's ports, though the blockade still had a severe impact on Yucatán's economy. In 1843, Yucatecans defeated the Mexican army when it tried to reimpose central rule. They took this opportunity to negotiate a return to the Mexican union, under the conditions that they could retain their own self-rule and constitution. Once again, Santa Anna violated the agreement, and Yucatán declared its independence again in 1846, remaining neutral during the U.S.-Mexican War.

In 1847, the Mayan Indian people launched a major uprising against Hispanic rule in Yucatán. The so-called Caste War succeeded in driving all Hispanic Yucatecans off the peninsula except for a couple of walled compounds. The Yucatecans appealed for international help in putting down the uprising. Eventually, Mexico came to the rescue, and Yucatán once again became part of Mexico in 1848. The Mayan uprising continued in earnest for more than 50 years, with skirmishes into the 1930s.

Commodore Moore was placed in command of the operation, with orders to capture Mexican towns and compel ransom payments; to force the inhabitants to make the payments, he was authorized to destroy public works and seize public property. But for the operation to come off at all, he had to work fast. Sam Houston had just been elected to another term as president, and Lamar and Moore feared he would countermand the deal as soon as he took office. On December 13, 1841, the very day that Houston was being sworn in as president, the Austin, San Antonio, and San Bernard sailed for Sisal, Yucatán. Houston issued an order recalling the ships two days later, but it was too late. For the moment, the navy was gone and beyond the president's reach. But Moore was well aware that his mission was flying in the face of Houston's disapproval. He wrote bitterly to his friend, General Albert Sidney Johnston, that he expected to be recalled and subjected to vicious political attacks.

When Moore got to Yucatán, he found the Yucatecans deep in negotiations with Mexico to end the rebellion. Moore recognized the possible peace as a tremendous threat to Texas and persuaded the Yucatecans to keep to their bargain with the Texas navy until they could make sure that Mexico and Santa Anna were sincere about wanting peace. He sent the San Antonio back to Texas with a full report on the situation for President Houston. He included a plea for the steamship Zavala to be repaired and sent south to shore up Texan control of the coast. The steamer was never sent. Texas had only a very small navy yard, and no one who knew how to work with the temperamental steam technology. Yucatán offered to pay for the repairs, but Houston refused. Instead, the Zavala was allowed to rot so badly that it was later deliberately run aground and wrecked in Galveston Bay rather than pay the cost of repairs. Houston would not even agree to sell the engines from the wrecked ship to raise money for the rest of the fleet.

Moore captured several Mexican ships, then received word of several disasters that to him confirmed that a more active course was needed. The news of the appalling mistreatment of the Santa Fe prisoners came at the same time as the Mexicans launched the first land assault on Texas since the Revolution, recapturing San Antonio. Moore didn't know it yet, but President Houston had issued him orders to blockade the Mexican coast, retroactively approving of his actions. Moore continued to wreak havoc on Mexican shipping near Veracruz until April 1842, when he ran low on money and provisions, and the men's terms of enlistment were running out.

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