1963-1966 Malaysian-Indonesian Confrontation

General Suharto on the cover of a 1966 TIME magazine
titled "Vengeance With a Smile"

In 1963, Achmed Sukarno, president of Indonesia, refused to recognize the new Republic of Malaysia. Therefore stirring a war between his nation against Malaysia. This undeclared war had no set battles, but low leveled guerrilla wars using paratroopers behind Malaysian lines, as well as underwater demolition teams to mine the harbor of Singapore. As the war was taking place, difference of opinions broke out in villages and homes, as the communists staged an overthrow of the current power (which failed). Most of the action took place on the divided island of Borne. 
General Suharto, Sukarno's general in chief, led the Indonesian forces against the communist rebels, leading them nationwide to wipe out all communists and leftists. This purge turned into a slaughter, estimating about 150,000 to about 500,000 communists dead. The leader of the leftists, Dipoa Nusuntara Aidit was killed, and the communists that had not yet been executed were thrown in prison cells in untold numbers. By 1976, it was recorded that there were still 70,000 political prisoners from this period held in prison. While the attempt at a communist takeover failed, the efforts dominated Indonesian military resources, and Sukarno agreed to reevaluate peace negotiations with Malaysia. A truce was declared on June 1, 1966 followed by a formal treaty signed August 11, 1966.