"The absence of official documentation and certain aspects of Suharto's early life that are inconsistent with that of a Javanese peasant (Suharto received, for example, an education fairly early on), has led to several rumors of Suharto being the illegitimate child of a well-off benefactor, which included a being the child of a Yogyakarta aristocrat or well-off Chinese Indonesian merchant. Western biographer R.E. Elson believes that such rumors cannot be entirely ruled out." - Suharto - Wikipedia, the free encyclopedia
Suharto learnt much about militarism from the Japanese army.
During World War II, Suharto worked for the Japanese controlled police force and then for the Japanese-controlled militia, the Peta.
In 1945, with the collapse of Japan, Sukarno and Mohammad Hatta declared the independence of Indonesia. This independence was not accepted by the Dutch or the British and led to conflict.
In 1946, Suharto became head of an Indonesian regiment stationed in Yogyakarta.
Reportedly, at this time, Suharto was involved in helping various mafias that traded in opium (heroin). - (Suharto - Wikipedia, the free encyclopedia)
In 1947 Suharto married Siti Hartinah, a Christian from a well connected family.
Siti Hartinah converted to Islam. She became known as 'Madame Ten Percent', a play on her name, Ibu Tien. When contracts were being given out she reportedly insisted on getting at least ten percent of the proceeds. Later, she was called 'Madame Fifty Percent'. (Ibu Tien Buried Today)
In 1949, most of Indonesia was given independence by the Dutch.
Between 1954 and 1959, Brigadier General Suharto was the commander responsible for Central Java and Yogyakarta provinces.
At this time he became friends with Chinese-Indonesian businessmen Liem Sioe Liong and Bob Hasan and was involved with them in various 'business enterprises'.
Suharto reportedly became involved in a 1959 smuggling scandal and he was transferred to the army Staff College in Bandung. Later, Suharto became commander of the key Kostrad regiment(Strategic Reserve). (Suharto - Wikipedia, the free encyclopedia)
Around 1956, the CIA and Britain's MI6 appear to have decided to topple Indonesia's President Sukarno, partly because he was 'non-aligned' rather than pro-American.
Indonesia did have a communist party, but in the world's biggest Moslem country, it was never likely to do particularly well in elections. The two biggest parties in Indonesia were Sukarno's Partai Nasional Indonesia and the Islamist party Masyumi.
Reportedly, the CIA had right-wing friends within the Indonesian military. (Indonesia 1957-1958 KH)
Suharto was in the right-wing camp.
The CIA and Britain's MI6 began to arm various rebel groups in Indonesia.
In 1958, rebellions began to break out in various parts of Indonesia.
William Blum, in his book Killing Hope (Indonesia 1957-1958 KH), wrote:
"CIA pilots took to the air to carry out bombing and strafing missions in support of the rebels...
"Sukarno later claimed that on a Sunday morning in April, a plane bombed a ship in the harbor of the island of Ambon-all those aboard losing their lives-as well as hitting a church, which demolished the building and killed everyone inside
"He stated that 700 casualties had resulted from this single run.
"On 15 May, a CIA plane bombed the Ambon marketplace, killing a large number of civilians on their way to church on Ascension Thursday...
"Three days later, during another bombing run over Ambon, a CIA pilot, Allen Lawrence Pope, was shot down and captured...
"He was to spend four years as a prisoner in Indonesia before Sukarno acceded to a request from Robert Kennedy for his release.
"Pope was captured carrying a set of incriminating documents, including those which established him as a pilot for the US Air Force and the CIA airline CAT."
The CIA and its friends did their best to undermine the Indonesian economy.
In 1965, some kind of coup took place in Indonesia. By 1966, Suharto had emerged as the country's leader. He became president in 1968.
In the months that followed the coup, army death squads, often recruited from Muslim and Catholic youth groups, murdered up to one million people.
Bali and other parts of Indonesia were awash with blood.
The CIA is reported to have given the Indonesian military lists of people who were to be dealt with.
"Former deputy CIA station chief Joseph Lazarsky and former diplomat Edward Masters, who was Martens' boss, said CIA agents contributed in drawing up the death lists" - [States News Service, 5/19/1990; Sydney Morning Herald, 7/10/1999; US Department of State, 2001 ]
According to Time Magazine, 17 December 1966 :
"The killings have been on such a scale that the disposal of the corpses has created a serious sanitation problem in East Java and Northern Sumatra where the humid air bears the reek of decaying flesh. Travellers from those areas tell of small rivers and streams that have been literally clogged with bodies."
Suharto now brought in his New Order government.
The military were to be the people who pulled the strings.
Every institution of any importance was to be dominated by the military. Everyone from cabinet minister to governors to village officials was likely to have a military connection. The military was to be involved in running various profitable businesses.
The USA stopped undermining the economy. Suharto allowed the USA and other western nations to invest and take control of many of the mining and other businesses in Indonesia.
1. The indonesian generals
2. Members of Suharto's Golkar Party.
3. Suharto's Chinese-Indonesian business friends.
4. The Suharto family
5. Investers in companies like Freeport, linked to Henry Kissinger, which has a gold mine in Indonesia.
The military and Golkar acted as intermediaries between businesses and the Indonesian government. "This led to bribery, racketeering, and embezzlement. Funds from these practices often flowed to foundations (yayasan) controlled by the Suharto family." 
Melody Kemp ( The good, the bad and the hopeful - reflecting on Indonesia ) wrote:
At least one third of the population of East Timor died as a result of the invasion. (East Timor Revisited: Ford, Kissinger and the Indonesian Invasion ... )
In 1998 Suharto was toppled, apparently by the CIA.
At some point in the 1990s Suharto was seen by some Americans as having become too powerful and too independent minded.
Suharto was giving too many business contracts to his family and Chinese-Indonesian cronies, rather than to American companies like Ford.
Some people in the Pentagon considered the possibility of having a general such as Prabowo or Wiranto or Yuhhoyono take over.
In order to topple Suharto there would need to be riots.
In Indonesia, in the years 1997- 1998, there were riots in various parts of Indonesia. Some riots looked spontaneous and some looked as if they had been planned. (http://www.insideindonesia.org/edit50/riots.htm)
In Indonesia, trouble is often organised by the spies. Back in the 1950s the British and American intelligence agencies had organised rebellions in various parts of Indonesia, in order to undermine President Sukarno.(http://www.westpapuanews.com/articles/publish/article_31.shtml)
In 1998 one of the key generals was Prabowo, son of Dr. Sumitro Djojohadikusumo, a former Finance Minister, said to have once worked with the British and the Americans against Sukarno.
In May 1998, Prabowo was commander of Kostrad, the strategic reserve, the regiment Suharto commanded when he took power in 1965.
General Wiranto, the overall head of the military, was seen as a rival to Prabowo.
The American Defence Secretary, William Cohen, was in Jakarta in January 1998 and he visited both Prabowo and Wiranto.
The CIA chief had also been a recent visitor to Jakarta. The CIA and the Pentagon were close to both Prabowo and Wiranto. (http://solidarity.igc.org/atc/emily75.html)
At the start of May 1998, students were holding peaceful demonstrations on university campuses across the country. They were protesting against massive price rises for fuel and energy, and they were demanding that President Suharto should step down.
On May 12th, students at Jakarta's Trisakti University, many of them the children of the elite, planned to march to parliament to present the government with their demands for reform. The police prevented the students from marching.
Some time after 5pm, uniformed men on motorcycles appeared on the flyover which overlooks Trisakti. Shots rang out. Four students were killed.
Riots of May 13-14
On the 13th of May there were reports of rioting in the area around Trisakti. President Suharto was attending a conference in Egypt and the military top brass went off to Malang in East Java to attend a ceremony.
On the 14th of May, serious rioting took place in the Jakarta area. There were no signs of any uniformed soldiers on the streets.
Over 1,000 people died during these Jakarta riots, most having been burnt in malls and supermarkets but some having been shot or beaten.
Alleged involvement of the military in planning the riots
Father Sandyawan Sumardi, a 40-year-old Jesuit priest and son of a police chief, led an independent investigation into the events of May 1998.
As a member of the Team of Volunteers for Humanitarian Causes he interviewed people who had witnessed the alleged involvement of the military in organising the riots and rapes.
A security officer alleged that Kopassus (special forces) officers had ordered the burning down of a bank;
a taxi driver reported hearing a man in a military helicopter encouraging people on the ground to carry out looting;
shop-owners at a Plaza claimed that, before the riots, military officers tried to extract protection money;
a teenager claimed he and thousands of others had been trained as protesters;
a street child alleged that Kopassus officers ordered him and and his friends to become rioters;
there was a report of soldiers being dressed up as students and then taking part in rioting;
eyewitnesses spoke of muscular men with short haircuts arriving in military-style trucks and directing attacks on Chinese homes and businesses.
There were reports of children being encouraged to enter malls and then of the malls being set on fire;
there were allegations that muscular men with short haircuts had gang-raped little Chinese girls and then murdered some of them.
Suharto told he had lost the support of the military
Some of Suharto's former allies deserted him. Wiranto allowed students to occupy Parliament. Reportedly Wiranto reported to Suharto on May 20th that Suharto no longer had the support of the army. Suharto was forced to resign on May 21 and was replaced by Habibie, his Vice President.
The continuing importance of the military
Wiranto remained as chief of the armed forces. Wiranto's troops began removing the students from the parliament building.
One result of the May riots was that the military appeared to remain the power behind the throne. In 2004, General Yudhoyono became president.