After the fall of President Soeharto in May 1998 Indonesia changed dramatically. Soeharto's Vice-President, B J Habibie, took over the presidency until October 1999, when Abdurrahman Wahid (Gus Dur) was elected. After only 21 months in office Wahid was impeached for alleged involvement in financial scandals and replaced by his Vice-President, Megawati Soekarnoputri, (the daughter of Indonesia's first President, Soekarno) in July 2001. The transition was a peaceful one, which was a promising sign that Indonesia was coming to terms with its new democratic system. Susilo Bambang Yudhoyono, Megawati's former security minister, was elected President in September 2004 after defeating Megawati in a second-round election run-off. Parliamentary and Presidential elections were held in April and July 2009 respectively.  President Yudhoyono was re-elected in the first round of the Presidential election with 60% of the vote – the first time an Indonesian President has been re-elected in democratic elections.   He was inaugurated for his second term on 20 October 2009.

 

There is a continuing threat from terrorism across Indonesia.  On 17 July 2009 two bombs exploded at the Ritz Carlton and Marriott hotels in Jakarta killing seven people.  On 1 October 2005, the second Bali bombing killed 20 people and injured many more. Other attacks against western interests in Jakarta include the Marriot Hotel bombing on 5 August 2003 and a car bomb outside the Australian Embassy on 9 September 2004.

 

On 12 October 2002 the first Bali bomb led to the deaths of 200 people, including 28 British nationals. A number of countries, including the UK, Australia and the US, are assisting Indonesia with police capacity building and counter terrorism training. 

 

The Indonesian government brokered an agreement (the Malino I Accord) to end fighting between Christian and Muslim factions in Central Sulawesi, which was signed on 20 December 2001. This has brought an end to the large scale inter-communal violence. Low level violence has continued in the region and the area remains volatile. The bombing of Tentena, a largely Christian town near Poso in Central Sulawesi, on 28 May 2005 killed 21 people. However stability has improved in recent years.  

 

In Maluku serious sectarian violence in 2000 and 2001 left thousands dead. On 12 February 2002 the Indonesian government brokered an agreement (the Malino II Accord) between Christian and Muslim factions in Maluku. On 15 September 2003 the Indonesian government lifted the state of civil emergency in the Province. However, sporadic clashes still occur.

 

The peace process in Aceh was a major achievement of President Yudhoyono’s first administration. Both parties fulfilled their security obligations under the peace agreement signed in August 2005. The Free Aceh Movement (GAM) handed in 840 weapons for decommissioning, and the Government of Indonesia withdrew all non-local military and police forces. The UK supported the peace process through its participation in the EU-led Aceh Monitoring Mission. Elections were successfully held on 11 December 2006 with a large turnout. Irwandi Yusuf, former GAM member, was elected as Governor of Aceh.  The 2009 elections were peaceful in Aceh, although there were allegations of intimidation in the run-up to them.

 

Following the departure of the Dutch and a brief period of UN administration, Indonesia took over the administration of Papua (formerly Irian Jaya) in 1963. Irian Jaya became a province of Indonesia following a UN-supervised Act of Free Choice in 1969, the legitimacy of which is much debated. The Special Autonomy law was passed after consultations with the Papuan people by Gus Dur's government on 1 January 2002. On 27 January 2003, President Megawati issued a Presidential Instruction to split Papua into three provinces. There was concern that this contradicted the Special Autonomy Law, making its implementation difficult. However, on 14 November 2003 the Indonesian government announced the formation of a new province of West Irian Jaya (now referred to as West Papua) in Papua marking the official split of West Papua from the rest of Papua.

 

In November 2004 the Constitutional Court ruled that the creation of West Irian Jaya was not legal. However the court also stated that the province was a de facto reality and should be recognised. President Yudhoyono reiterated this position in a speech made to the DPD (Regional Government Assembly).  The government subsequently issued a regulation on 16 April 2008 which clarifies the status of the province of West Papua and puts it on an equal footing with that of the province of Papua.