Issues over this period have included a push for a stronger democracy and civilian rule, elements of the military trying to retain their influence, a growing Islamism in politics and society, and demands for greater regional autonomy.

The Reformasi of 1998 led to changes in Indonesia's various governmental institutions, including the structures of the judiciary, legislature, and executive office.

Generally, the fall of Suharto in 1998 is traced from events starting in 1996, when forces opposed to the New Order began to rally around Megawati Sukarnoputri, head of the PDI and daughter of the founding president Sukarno.

[6][7] Growing dissatisfaction with Suharto's authoritarian rule and the rapid erosion of the economy led many, chiefly the younger generation, to renew their protests directly against the New Order.

People were burning everything within the city, including cars, motorcycles, buildings, and monuments in addition to pillaging and looting from stores.

Political prisoners such as Sri Bintang Pamungkas, Muchtar Pakpahan, and Xanana Gusmão were also released under Habibie's orders.

[10] Wahid intended to give rebellious Aceh province a referendum on various modes of autonomy, rather than an option for independence like in East Timor.

Two months later in May, the government signed a memorandum of understanding with GAM to last until the beginning of 2001, by which time both signatories would have breached the agreement.

In March of that year, Wahid suggested that the 1966 Provisional People's Consultative Assembly (MPRS) resolution on the banning of Marxism–Leninism be lifted.

At the same time, Wahid was also accused of keeping a US$2 million donation made by the Sultan of Brunei to provide assistance in Aceh.

At the end of November, 151 People's Representative Council (DPR) members signed a petition calling for the impeachment of Wahid.

[23] Nevertheless, NU protesters continued to show their support for Wahid and in April, announced that they were ready to defend and die for the president.

By July, Wahid grew desperate and ordered Susilo Bambang Yudhoyono (SBY), the Coordinating Minister for Politics and Security to declare a state of emergency.

The TNI, having had a bad relationship with Wahid through his tenure as president, stationed 40,000 troops in Jakarta and placed tanks with their turrets pointing at the Presidential Palace in a show of force.

Wahid continued to insist that he was the president and stayed for some days in the Presidential Palace but bowed down and left the residence on 25 July to immediately fly to the United States for health treatment.

Under Megawati Sukarnoputri, the daughter of Indonesia's first president Sukarno, the process of democratic reform begun under Habibie and Wahid continued, albeit slowly and erratically.

Megawati appeared to see her role mainly as a symbol of national unity, and she rarely actively intervened in government business.

Under her tenure, the Mutual Assistance Cabinet (Indonesian: Kabinet Gotong Royong) helped govern the country.

Consisting of 36 ministers, it included members of the Democratic Party, Golkar and the PPP, PBB, PKB, PAN, PKP, and PKS.

In May 2008, rising oil prices contributed to SBY's decision to cut fuel subsidies once more, which were the subject of protests in May and June 2008.

SBY allowed Jakarta governor Sutiyoso to open the Manggarai watergate with the risk of flooding the Presidential Palace.

In 2014, constitutionally barred from running for a third term, SBY was succeeded by Joko Widodo (popularly known as Jokowi) with Kalla returning as vice president, defeating Prabowo and Hatta Rajasa.

[38][39] A controversial remark by his former deputy governor Basuki Tjahaja Purnama (Ahok) led to divisions in the country's Muslim population amid a gubernatorial election.

There have been concerns of declining freedom of expression during this period, evidenced by the arrest, detainment, and imprisonment of many people for their social media activity being interpreted as an insult to the president and the government.

[43][44][45][46][47] Several disasters, such as earthquakes (In Palu, Lombok, and Banten) and a haze due to deforestation in Borneo and Sumatra occurred during this period.

[50] Jokowi and his vice presidential candidate Ma'ruf Amin won the election against Prabowo and his running mate Sandiaga Uno.

[52] On 16 August 2019, forty-three Papuan students in Surabaya, East Java were arrested by police following reports that an Indonesian flag was damaged outside the building where they lived,[53] leading to protests in Papua and other parts of Indonesia.

[54] A series of mass demonstrations led by students took place in major cities of Indonesia in September 2019 to protest against new legislation that reduces the authority of the Corruption Eradication Commission (KPK), as well as several bills.

[55] The protests subsequently developed into the largest student movement in Indonesia since the 1998 demonstrations that brought down the Suharto regime.

[56] On 26 August 2019, President Joko Widodo announced that the country's new capital city will be located in East Kalimantan on Borneo island.