After the Spanish regained control of Cuzco, Manco Inca (The Inca Emperor) and his armies retreated to the fortress where he successfully launched attacks against Pizarro based at Cuzco and even managed to defeat the Spanish in an open battle. However, the Inca Emperor knowing that he could not fight a war in which almost everyone one of his people died from fled to the south in the mountains in Vilcabamba. There they founded a new Inca Empire which would remain independent for some decades. Tupac Amaru was the last Inca Emperor, he would later be murdered and the Spanish would take over Vilcabamba, even the Spanish King didn 't like this final destruction of the Inca Empire and did not want his death. However the Viceroy of Peru killed him