Following a lengthy recuperation in Cuba, traveling on a false passport Guevara entered Bolivia in November of 1966, again with the idea of organizing a revolt and hoping to topple Bolivia's pro-U.S. military government and installing a Communist government there. A parcel of jungle land in Nancahazu was purchased by native Communists and turned over to him for use as a training area. The evidence suggests that this training was more hazardous than combat to Guevara and the Cubans accompanying him. Little was accomplished in the way of building a guerrilla army. On learning of his presence in Bolivia, President Rene Barrientos is alleged to have expressed the desire to see Che's head displayed on a pike in downtown La Paz. He ordered the Bolivian Army to hunt Guevara and his followers down.
Che and his insurrectionists found themselves cornered in Bolivia, the American aid to the Bolivian government on one end, and the lack of assistance from his allies. In addition to this, the CIA also helped anti-Castro Cuban exiles to set up interrogation houses for those Bolivians who were thought to be assisting Che Guevara and/or his guerillas, which were often used for torture of these individuals.
The anti-insurrectionists were notified of the location of Guevara's guerilla encampment by a deserter; and on October 8th, 1967the encampment was encircled and Che was captured while leading a patrol in the vicinity of La Higuera, Bolivia. His surrender was offered after being wounded multiple times in the legs and having his rifle destroyed by a bullet. According to soldiers present at the capture, during the skirmish, as soldiers approached Guevara, he shouted, "Do not shoot! I am Che Guevara and worth more to you alive than dead." Barrientos ordered his execution immediately upon being informed of Guevara's capture. Guevara was summarily executed; he was taken to a rugged old schoolhouse and bound by his hands to a board. Supposedly, Ernesto Guevara did have some last words before his death; he allegedly said to his executioner, “Shoot, coward, you are only going to kill a man,” after which he was shot in the heart.
A CIA agent and Veteran of the US invasion of Cuba at the Bay of Pigs, Felix Rodriguez, heard of Guevara's chapter and relayed the information to the CIA. He has said on multiple occasions that he was the one that shot Guevara. This is generally thought to be untrue. After the execution, Rodriguez took Che's Rolex watch, often proudly showing it to reporters during the ensuing years. Guevara died on October 9th. He was buried in an unmarked grave in the vicinity of the execution site after the CIA had removed his hands to send to different parts of the world to ensure his identity.
Also removed was Guevara's diary, which outlines the guerrilla war being fought in Bolivia. It tells of the group being forced to begin operations due to discovery by the Bolivian Army, the eventual and accidental split of the group, and the general failure of the guerrilla. It shows the split between Guevara and the Bolivian Communist Party that led the guerrilla to have significantly less soldiers than originally anticipated. It shows that Guevara had a great deal of difficulty recruiting the local populace due mainly to the fact that the guerrilla group had learned quechua and not the local language. As the campaign drew to an unexpected close, Guevara was becoming increasingly sick. He suffered from asthma, and most of the guerrilla's last offensives were carried out to obtain medicine for the sick leader.
From the group of 27 guerrillas that set out on Febuary 1, 1967, only 3 survived after October 9, 1967. They crossed the Andes Mountains into Chile. There, they were met by Salvador Allende, who gave them asylum and helped them reach Cuba.
In 1999, the skeletal remains of Guevara's body were exhumed, positively identified by DNA matching and returned to Cuba, where he is revered as a heroic revolutionary leader.