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In 1839, he was made political chief of the department of San José. He fought in the "Guerra Grande" against Manuel Oribe and his Argentine backers. He became a leading figure in the Colorado Party and formed a triumvirate with Fructuoso Rivera and Juan Antonio Lavalleja in 1853.:21
He served as interim President of Uruguay and remained in power until Aug. 1855, when overthrown by the Blanco president Manuel P. Bustamante, which resulted in civil war and Flores taking refuge in Argentina.:21
In 1863, he started a rebellion (Cruzada Libertadora or Crusade of the Liberator) against the Blanco president Bernardo Berro, which led to civil war in Uruguay.:24 With Argentinian and Brazilian help, by February, 1865 he had taken Montevideo.
He established a provisional government, a term used to disguise his personal dictatorship. Although the Uruguayan Colorado Party has the reputation of being progressive and democratic, Flores and other Colorado Party leaders of the 19th century, and many prominent 20th century Colorado leaders, collectively demonstrated by their actions that they were comfortable with rule by decree, with power not unusually concentrated in very few people. The tendency of some observers to describe Latin American heads of state who ruled by decree as 'de facto' Presidents may be seen in this light. During his rule, Flores joined Brazil and Argentina in the devastating Paraguayan War.
Flores's government ended on February 15, 1868.
Four days after stepping down as President, he was murdered by a group of unidentified assassins. But although Flores' killers were not formally identified, it may be added that as a background to his assassination is the intermittent Uruguayan Civil War which continued throughout much of the 19th century between Colorados and Blancos.
More broadly, his period of office continued a tendency already present among at least some Colorado presidents but surviving virtually to contemporary times, for the national leadership under that party to be nominally liberal in doctrine but actually highly authoritarian. In this sense, Flores was definitely in the 'Riverista' mold, after Fructuoso Rivera, rather than in what would much later be referred to as a 'Batllista', after the liberal José Batlle y Ordóñez.
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| President of Uruguay