Alvarado went to Santo Domingo in 1510 and in 1518 he commanded one of Juan de Grijalba's ships sent from Cuba to explore the Yucatan Peninsula. In February 1519 he accompanied the army, led from Cuba by Hernán Cortés, who was going to conquer Mexico. Alvarado was first put in charge of Tenochtitlan (later Mexico City) in 1520 when Cortes left the city to meet a rival Spanish force on the coast. When the Aztecs gathered in the square to celebrate the Toxcatl festival, Alvarado feared an uprising and ordered his men to attack first. About 200 Aztec chiefs were massacred by Alvarado's men, who in turn were besieged in their rooms by an angry crowd. Upon his return, Cortes learned of the attack and the uprising and quickly planned a nightly retreat from Tenochtitlan. On the night of June 30, 1520, known as sad comonoche ("sad night"), Cortes and his men try to leave the city in silence, but were seen by the Aztecs. Fierce fighting broke out, and Alvarado, who led the rearguard, escaped by little, thanks in large part to a spectacular jump through a canal. The Spaniards recaptured Tenochtitlan in 1521, and in 1522 Alvarado became the first mayor of the city (mayor or chief magistrate).
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