It is a bitter irony that the first direct presidential election to be held in Indonesia has resulted in another general taking power.

Although the official results will not be made public until 5 October, it is already clear that Susilo Bambang Yudhoyono won comprehensively against Megawati Sukarnoputri. The reasons are not difficult to fathom.

Although she had the advantage of being the incumbent, Megawati was a huge disappointment as president and was surrounded by unsavoury characters, not least her husband, Taufiq Kiemas, a man renowned for corruption and double-dealing. Yudhoyono on the other hand was able to present himself as a clean and incorruptible politician whose demeanour in the run-up to the election on 20 September won plaudits from commentators and the press. There was no civilian politician to match him.

The 2004 presidential election established a new tradition. By and large, voters did not cast their votes in accordance with political party affiliation; they voted according to personal preferences. The decision by Akbar Tanjung, the leader of Golkar, along with the leaders of other parties from the Suharto era, to back Megawati's presidential bid, failed to secure her election. This is likely to lead to a major overhaul in the leaderships of Golkar and the PDI-P, Megawati's party.

However, the presidential election shows clearly that the military continue to play a very significant role in political affairs in Indonesia. In the first round held in July, five teams competed to become president and vice president and of the ten contestants, five were from the military. As none of the contestants broke through the fifty per cent threshold, a re-run was held on 20 September.

While Yudhoyono succeeded in projecting the image of a democrat and has frequently spoken of the need for the reform of the armed forces, his military career reveals him as a man with a strong sense of dedication to the military's role in society.

When he first joined the army, his idol was Sarwo Edhie whom he once extolled as "the epitome of a true soldier". Sarwo Edhie was one of the most ruthless officers to serve under Suharto. He was largely responsible for the massacre of hundreds of thousands of communist suspects in 1965-1966, and later played a leading role in crushing Papuan resistance in the run-up to the Act of Free Choice in 1969. Yudhoyono subsequently married Sarwo Edhie's daughter.

Yudhoyono has served twice in Kostrad, the Strategic Army Command, first as commander of an airborne battalion and later as commander of one of its infantry battalions. He did two tours of duty in East Timor under Indonesian occupation, was commander of the Yogyakarta military command and served for a period in the UN peace-keeping force in Bosnia.

In the mid-1990s, he was chief of staff of the Jakarta military command, a position that he occupied when troops under his command took part in an assault on 27 July 1996 on the headquarters in Jakarta of the PDI (the previous name of the PDI-P), the party chaired by Megawati. The attack resulted in a number of fatalities yet the incident has never been investigated and no one has been called to account. As always, the military have been safeguarded from any accountability because of the impunity they continue to enjoy.

After retiring from the army with the rank of lieutenant-general in 2000, Yudhoyono became Minister-Coordinator for Politics and Security in the government of Abdurrahman Wahid. This appointment was criticised by several human rights organisations; Hendardi, director of the human rights organisation, PBHI, warned that it would jeopardise attempts to investigate the role of the army and of Yudhoyono in the 27 July 1996 attack.

Hendardi was also critical of the presence of a military officer as a top-ranking member of Wahid's government. Even so, Yudhoyono subsequently held the same position in the government of Megawati, after Wahid resigned, facing the threat of impeachment.

Yudhoyono surrounded himself with a number of retired military officers in the kitchen cabinet which assisted him in his presidential bid. They include:

• Major-General Sudi Silalahi, an assistant to the commander of the Jakarta garrison in 1998, who allegedly helped provoke riots and the burning of shops and businesses while troops looked, just before Suharto's downfall. In 2000, when he was military commander in East Java, he allowed thousands of members of an extremist Muslim group, Laskar Jihad, to travel from Surabaya to Ambon to join clashes between Muslims and Christians
• former defence minister under Suharto, General Edy Sudradjat
• Suharto-era Minister for State Empowerment Lieutenant-General T.B. Silalahi, closely associated with the business tycoon Tomy Winata who has successfully brought defamation charges against several journalists
• former intelligence chief under Suharto, Major-General Syamsir Siregar
• Admiral Widodo who was commander in chief of the armed forces and Minister-Coordinator for Political and Security Affairs
• former chief of staff of the armed forces for social-political affairs Lieutenant-General Moch Ma'ruf. These men could well be appointed to key cabinet positions, such as heading the interior or defence ministries.

One of the most controversial bills awaiting adoption is the armed forces bill which, as presently drafted, will give the military special powers in conditions of an emergency. Under such circumstances, men like these with experience in both military and civilian posts, could reverse the advances towards democracy that have been achieved since the fall of Suharto.

While Yudhoyono has often spoken of the need for the reform of the armed forces, nothing has come of these intentions although he has had plenty of opportunity as a senior member in two post-Suharto cabinets to put his words into action.

Although Yudhoyono has announced that his government will take action to combat widespread corruption and attempt to reverse the country's economic decline, it remains to be seen whether he can achieve these objectives.

The key issues on which his presidency will be tested are:

• Resolving the conflict in Aceh by peaceful means, through the resumption of peace talks with GAM, the Free Aceh Movement, and ending the current military operations there.
• Reversing the decision to split West Papua into three provinces which has provoked widespread criticism from Papuans, and agreeing to enter into dialogue with Papuan representatives on a range of issues, including the future political status of West Papua.
• A thorough overhaul of the draft law on the armed forces, in particular reversing the provision that allows serving officers to hold positions in national and local administrations.
• Announcing a firm commitment to uphold basic human rights, in particular freedom of the press and freedom of expression, and seeking a reversal of a court decision to sentence the editor of Tempo to a one-year prison term on a charge of defamation.
• Announcing a firm commitment to overhaul and cleanse the judiciary, and announcing a commitment to the rule of law and the ending of impunity.