Siyono’s wife Suratmi probably did the best thing she could when she asked for help from Muhammadiyah, Indonesia’s second largest Islamic organization, to figure out why her husband died in the custody of the Indonesian police’s feared counter-terrorism squad Densus 88 last month.

Along with her effort to seek for the truth through Muhammadiyah, she also handed over a folded brown paper bag which she said was given by Densus 88 after her husband’ death. Muhammadiyah in a press conference said the paper bag was loaded with Rp100 million (US$7,606) as a “token of sorry” to Siyono’s family.

The 34-year-old Siyono, who like many Indonesians has one name, was a resident of Dukuh village in Klaten, Central Java. He was arrested on allegations of involvement in terrorism on March 8 and died in custody on March 10. He was buried on March 13.

He is the 121st person to have died after being arrested by Densus 88 since the elite police unit for counterterrorism was established on Aug. 26, 2004, according to data from the National Commission on Human Rights (Komnas HAM). The unit, comprising 400-500 personnel, was established on funds by the US State Department, which paid for its weapons, salaries, high-level training in communications interception, close combat warfare and intelligence gathering and analysis.

The unit is given credit for turning the tide in Indonesia’s war against the terrorist organization Jemaat Islamiyah. It has now come into the spotlight because of intensifying fears that Indonesians who have slipped out of the country to the Middle East to join the Islamic State, known as ISIS, or Daesh, would be coming home to wreak domestic mayhem. By one estimate, 500 Indonesians are in the Middle East. Some 200 – mostly women and children – have been caught in Turkey and sent back to be kept under surveillance. January attacks in central Jakarta, which took eight lives including four of the attackers, were said to have been organized and funded by Bahrun Naim, an Indonesian computer expert believed to be in Syria.

Densus 88’s reputation for effectiveness hasn’t been without cost. It has come under scrutiny by human rights groups for its reputation for torture and for “shootouts” with terrorists that may not have been shootouts at all but executions. In 2010, the unit came under fire for a video showing members pressing a smoldering stick against a Papuan separatist’s genitals, a plastic bag wrapped around the suspect’s head, and one officer holding a large knife next to the pleading suspect’s neck.

The police first told a different story about Siyono, whom they said had stashed a handgun and attacked officers while being taken by Densus 88 to a location in Yogyakarta in early March. A scuffle broke out inside the car and Siyono bumped his head, which led to his death, they said.

But an autopsy by doctors affiliated with Muhammadiyah which was conducted at the request of Siyono's wife revealed he died from blunt trauma to the chest, which broke bones near his heart. The autopsy also found no defensive wounds on his body.

After these revelations, the national Police spokesman Insp. Gen. Anton Charliyan on April 5 told reporters the counterterrorism unit had committed several “procedural mistakes” and that this would be investigated.

The House of Representatives plans to summon the chiefs of the National Police and the National Counterterrorism Agency (BNPT) to explain a series of deaths involving Densus 88 and terror suspects in recent years.

"The questions are whether Siyono was indeed a terrorist who warranted arrest, and whether he died because he resisted," said Desmond Mahesa, deputy chairman of House Commission III, which oversees human rights issues, as quoted by local media.

"We plan to meet on Wednesday with the BNPT and next week with the National Police," the Gerindra Party lawmaker said during a hearing with representatives from Komnas HAM and Muhammadiyah.

The January bombings and shootings show that terrorism remains a threat to Indonesia’s security despite ongoing counterterrorism measures.

Unnecessary abuses during current counterterrorism operations have highlighted the need for clearer operating procedures for the police. Alleged violations in the arrest and detention of Siyono have heightened concerns that human rights will be compromised from these counterterrorism measures is something real and must be prevented.

Despite ongoing terrorist incidents in areas across Indonesia, the government’s plan to revise the 2003 Terrorism Law has drawn concern and criticism, primarily on its potential for rights abuses. In the law’s draft revision, security institutions have wider authority to take measures against persons suspected of terrorist activities.

The 2003 law was a government response to terrorist attacks in Indonesia, which began to intensify after bombings in Bali in 2002 which killed 202 people, mostly foreign tourists.

Coordinating Political, Legal and Security Minister Luhut Pandjaitan said the law revision would give security personnel authority they should have in handling terrorist offences. He said the law revision would empower security elements so that they could take the necessary measures for suspected terrorists. However, he guaranteed that the revision would not be similar to the Internal Security Act (ISA) adopted by Malaysia and Singapore, two neighboring countries widely known for their tough measures in tackling terrorism.

Aside from general success in handling terrorism in Indonesia, there has been a growing concern on the rise of military involvement in the counter-terrorism effort which has been “politically given” to the police to handle.

The decision to give full authority to the police to handle terrorism instead of the military was originally to avoid civilian casualties during its process. However, too many wrong arrests and erased terror suspects has raised concerns over how the police have been handling the issue.

In the past few years, terrorist cells in Indonesia have shifted their target from foreign interests to police officers, who they refer to as the “more immediate enemy.”

At the moment, around 2,000 military and police personnel are searching for the militant leader Santoso, who has publicly pledged loyalty to ISIL. He is considered the most wanted terrorist in the country, and his fighters have been on the run for more than three years in the jungles of Central Sulawesi, as part of Operation Tinombala 2016.

The recent involvement of the Indonesian military (TNI) on the chase was after the police realized that they lacked the capability in jungle warfare to be able to do the task. Police chief Badrodin Haiti originally requested that the army raiders and Special Forces train the mobile brigade in jungle warfare.

According to a recent report from Institute for Policy analysis of Conflict (IPAC) the request was passed to the TNI chief, General Gatot, who apparently agreed but then had second thoughts – perhaps not wanting to be accused of militarizing the police and probably not wanting to weaken the case for military engagement in internal security.

The TNI then responded by sending a 60-person special forces (Kopassus) team and a 40-person combat intelligence platoon from the army strategic reserve of command (Kostrad) for training last September.