Violent extremism in Indonesia continued to be low-tech and low-casualty, but groups continued to proliferate from Sumatra to Sumbawa, and there seemed to be an inexhaustible supply of recruits. The typical terrorist suspect was not a mass killer with global ambitions; he was more likely to be one step up from a petty criminal whose efforts to make simple pipe bombs almost always failed. There were no women among the 66 arrested and 21 suspects killed during 2013. One attempted suicide bombing killed only the bomber. Guns were in high demand, used for fund-raising robberies and revenge attacks on police — terrorists managed to kill three officers, down from eight in 2012. While police continued to be the primary target, several plots were hatched, all unsuccessful, to avenge attacks on Muslims in Myanmar. Despite the generally low capacity of wouldbe terrorists, however, concerns were mounting that three factors could lead to new enthusiasm for jihad at home: anger over deaths of suspects in police operations; releases from prison of convicted extremists; and the return of Indonesian fighters from Syria.

Most of the Islamist violence during the year was attributable to two networks, the Mujahidin of Eastern Indonesia (Mujahidin Indonesia Timur, MIT), based in Poso, Central Sulawesi, and the Mujahidin of Western Indonesia (Mujahidin Indonesia Barat, MIB), based in greater Jakarta and West Java. Both were alliances that included splinter groups of Darul Islam, the venerable sixty-five-year-old Islamic insurgency, and defectors from JAT, but the two were not formally linked. At year's end, MIT was still alive, if besieged; MIB had been largely crushed. The once-feared Jemaah Islamiyah, which since 2007 had disengaged from violence in Indonesia, was reburnishing its reputation as a jihadi organization through its channels to Syrian Islamist rebels.

In addition to Islamist groups, a tiny but growing anarchist movement with international links launched a number of arson attacks across the country from Jakarta to Aceh to South Kalimantan. The media paid no attention, much to the chagrin of those involved.

Mujahidin of Eastern Indonesia

MIT, led by Santoso alias Abu Wardah, a former member of JI's affiliate in Poso, grew out of a JAT military cell in Central Sulawesi that was formed in 2010 in the aftermath of the break-up by police of a militant training camp in Aceh.