After the facts, Bolivar continued to govern in a rarefied environment, cornered by fractional disputes. Uprisings occurred in New Granada, Venezuela, and Ecuador during the following two years. The separatists accused him of betraying republican principles and of wanting to establish a permanent dictatorship. Gran Colombia declared war against Peru when president General La Mar invaded Guayaquil. He was later defeated by Marshall Antonio José de Sucre in the Battle of the Portete de Tarqui, 27 February 1829. Sucre was killed on 4 June 1830. General Juan José Flores wanted to separate the southern departments (Quito, Guayaquil, and Azuay), known as the District of Ecuador, from Gran Colombia to form an independent country and become its first President. Venezuela was proclaimed independent on 13 January 1830 and José Antonio Páez maintained the presidency of that country, banishing Bolivar.
On 20 January 1830, as his dream fell apart, Bolívar delivered his final address to the nation, announcing that he would be stepping down from the presidency of Gran Colombia. In his speech, a distraught Bolívar urged the people to maintain the union and to be wary of the intentions of those who advocated for separation.
Bolívar finally resigned the presidency on 27 April 1830, intending to leave the country for exile in Europe. He had already sent several crates containing his belongings and writings ahead of him to Europe, but he died before setting sail from Cartagena.