Prabowo Subianto could end up as Indonesia's president by the end of the week. Crikey intern Paul Millar trawls through diplomatic cables released by WikiLeaks and finds distressing allegations.

“To say that Prabowo has a controversial reputation is an understatement.”

So reads a US diplomatic cable released by WikiLeaks. The retired Indonesian general and disgraced special forces commander may become one of Australia’s most important allies in the Asia-Pacific region if he defeats Jakartan governor Joko “Jokowi” Widodo in tomorrow’s presidential poll. While the latest Roy Morgan poll shows Jokowi clutching to a narrow lead of 52-48, Prabowo’s meteoric surge of support over the last two months could be enough to make him the leader of the world’s third-largest democracy.

Gerindra party candidate Prabowo Subianto rose to military power under the autocratic Suharto administration, which ruled Indonesia for more than 30 years. Rising through the ranks of Kopassus, the Indonesian special forces, Prabowo soon developed a reputation for brutal and uncompromising tactics in putting down perceived threats to Suharto’s authority. Although they later divorced, Prabowo’s marriage to Suharto’s daughter Titiek bound him closer to the regime and gave him the resources he would later channel towards his bid for political office.

The diplomatic documents revealed by WikiLeaks serve as a bleak reminder of the manner in which Prabowo retired from military service.

Prabowo was dishonourably discharged from active service following his role in the abduction of youth leaders, political opponents and pro-democracy activists carried out in the lead-up to the May 1998 riots that marked the fall of Suharto. An estimated 23 protesters were forcibly taken at gunpoint by Tim Mawar (“Rose Team”), a covert unit under the command of Kopassus. The nine demonstrators who were later released testified to beatings, electrocution and drownings at the hands of their captors. Fourteen were never found.

Although Prabowo later admitted to authorising the kidnapping of nine of the activists, a military tribunal ruled that Tim Mawar had been acting on its own authority. Prabowo was expelled from service for failing to control his subordinates and fled into self-imposed exile to Jordan a step ahead of the courts.

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The leaked cables also make startling allegations about Prabowo’s actions during the riots themselves, outlining how he was a key player in the struggle among the military elite to become Suharto’s successor:

“International NGOs have called for Prabowo’s prosecution for alleged atrocities committed in East Timor by forces under his authority in 1999. He was also in command of forces in May 1998 in Jakarta. These forces allegedly tried to create chaos in the city as part of an effort by Prabowo to seize power for himself. During this timeframe, dozens of Indonesians died in mysterious fires and Indonesian Chinese were victimized, especially in the area of Glodok, Jakarta.”

Perhaps most damning are references to Prabowo’s close association with Muchdi Purwoprandjono, another special forces commander and later intelligence officer who served with the future presidential candidate in East Timor and regions. Described in the cables as “one of Indonesia’s most vindictive public figures”, Muchdi succeeded Prabowo as Kopassus’ commander in March 1998 and was heavily implicated in his share of disappearances during the chaos. Of the nine people who disappeared during the 53 days of his command, four were never found. The cables mention rumours that they were killed and buried beneath the asphalt of the airport highway, along with the other 10 who vanished. Stripped of his position by the same tribunal that condemned Prabowo, Muchdi was relegated to a headquarters staff officer position.

Rising through the ranks of the Indonesian State Intelligence Agency (BIN), Muchdi was charged with orchestrating the 2004 murder of human rights activist Munir Thalib. Muchdi was acquitted of all charges in 2009 when many of the witnesses retracted sworn statements implicating him. No witnesses were offered any form of protection during the trial.

Muchdi is widely regarded as a protege of Prabowo, maintaining the brutal tactics and autocratic ambitions of his predecessor. Both devout Muslims with a strong military background, the pair served as the inner elite of Gerindra (the Great Indonesia Movement Party), the political party formed by Prabowo after his return from exile.

A diplomatic cable from 2008 described the former deputy chairman of BIN as a remorseless figure.

“A retired general who knows Muchdi well described him to DepPol/C as ‘crazy’, explaining that he has a gigantic ego and no scruples. The former head of the Munir case police investigation team, Internal Affairs head Bambang Hendarso Danuri (recently named as the President’s choice to be the next national police chief) told DepPol/C that Muchdi has a personality that would allow him to commit human rights violations without it bothering him.”

Although Muchdi left Gerindra in 2011 for undisclosed reasons, the two men still maintain a close friendship.

Tomorrow, 187 million Indonesian voters will decide which man will lead the world’s third-largest democracy into the Asian century. If Prabowo Subianto emerges triumphant, Australia may find itself wondering what enemies it needs with friends like these.