Below is an article published by The Jakarta Globe:

The sun was rising slowly behind Salahutu Mountain but the island of Ambon remained dark as thunder-infested clouds hid the rays overhead. 

A storm was brewing quickly, with drops of rain visible just over the horizon on the Banda Sea. The air felt cold in the middle of Ambon’s rainy season, and as I traveled with my guide on a one-hour motorbike ride, my body shivered uncontrollably. 

I gripped my jacket tighter around my body as I glanced briefly at the reflection of my guide, Rezon, on the side mirror of his motorbike. He seemed accustomed to the low temperature, wearing sandals, shorts and a thin T-shirt with a printed image of the Spice Islands. 

“This is where we are, and this is where we are headed,” he said, pointing to the lower-left side of the printed part on his T-shirt. 

I was on my way to meet a pro-Maluku independence activist, a man who chooses to be identified only as Geba, which means “friend” in the local dialect. 

I had met him a day earlier at a small coffee shop in Ambon city, tucked away in a secluded section of a frantic market. Chatting over a cup of coffee, he recounted how Malukans had lost much of their rightful wealth — first robbed by the Europeans, who profited from centuries with a monopoly on the islands’ spices, and later by the Indonesian government, which siphoned Maluku’s natural resources to develop Jakarta. 

But Geba, who claims to be a proud member of the outlawed South Maluku Republic (RMS), had wanted to return to his own home before showing me a more sinister side to his struggle. 

“I have paid a hefty price for my fight,” he said when we met for the second time, sitting on his back porch. 

Carefully unbuttoning his shirt, he revealed scores of burn marks all over his chest, stomach and back, each the size of a cigarette butt. 

“Hundreds of times, the police burned me with a lit cigarette,” he said, recalling the time he spent in detention in 2006 after organizing an RMS ceremony, during which the banned Benang Raja flag had been unfurled. 

The RMS activist said his captors told him to lie with his face down and his body flat across two chairs, allowing police officers to kick his back with their boots. 

“They also hit me in the head with the butt of a rifle,” he said. “I was kicked in the neck, too, and they smashed a glass on my head. Even with blood gushing from my head and three sets of my teeth broken, the torture didn’t stop.” 

Geba identified his tormentors as members of the National Police’s Special Detachment 88 (Densus 88), an elite unit more often associated with fighting terrorists and militants than people accused of peacefully protesting for independence. 

Densus 88 was formed shortly after the 2002 Bali bombings that killed 202 people, mostly foreign tourists. The counterterrorism unit began attracting foreign donors and training agreements, making it the most elite unit in the police force. 

It is easy to distinguish an ordinary police officer from a member of the Densus 88. While most officers hold locally made Pindad assault rifles or handguns, Densus 88 officers carry anything from Austrian Steyr AUG assault rifles to the reincarnation of the M16 rifle, the AR-15. 

With terrorism threats waning in the years after the second Bali bombing in 2005 — there were only minor incidents in the provinces, like the bombing of a pig market in Poso, Central Sulawesi, and a series of ambushes against law enforcers in Ambon — so too did Densus 88’s once prominent role begin to fade. 

It was a few years before Indonesia was rocked by another major terrorism incident: the twin suicide attacks at the JW Marriott and Ritz-Carlton hotels in Jakarta in 2009. 

“Ideally, they [Densus 88] should keep focusing on cracking down on the terrorism network,” said Taufik Andrie, the research director of security think tank the Institute for International Peace Building (YPP). 

“But we cannot dispute the fact that [Densus 88] are more equipped with the tactical know-how and gadgetry to conduct investigations more effectively than other police units.” 

In June 2007, the counterterrorism unit was involved in the arrest of 22 RMS activists accused of unfurling the Benang Raja flag in front of President Susilo Bambang Yudhoyono. 

Eva Kusuma Sundari, a lawmaker from the Indonesian Democratic Party of Struggle (PDI-P) and a member of the legislature’s Commission III, which oversees the National Police, said the counterterror unit has even investigated banking crimes. 

“I have met with some of the officers personally and they said they were involved in evaluating banking crime cases that were dropped by the police,” she said. 

With the death of major terrorism suspects Noordin M. Top and Dulmatin, and with terrorist figures like Abu Bakar Bashir, Umar Patek and Abu Umar behind bars, Densus 88 is now stepping up its engagement in non-terrorism issues again. 

In August last year, counterterrorism officers were deployed in conflict-riven Papua after four people were killed in an ambush by suspected armed separatists in Nafri village, on the outskirts of Jayapura. 

“We have dispatched crime scene investigators and Densus 88 officers to Nafri to help Papua police hunt for the perpetrators,” said then-National Police spokesman Insp. Gen. Anton Bachrul Alam. 

Oktovianus Pekei, a Papuan priest in the district of Paniai, said suspected counterterrorism officers also raided people’s homes in the district capital, Enarotali, during a standoff with members of the armed rebel movement, the Free Papuan Organization (OPM) in November. 

“The police officers in Paniai were different from Brimob, although police say they were Brimob,” he said, referring to the police’s paramilitary unit, the Mobile Brigade. 

“These officers [in Paniai] wore ski masks and heavy combat gear and helmets. They also carried sophisticated weaponry and state-of-the art equipment.” 

Activists in West Nusa Tenggara said Densus 88 officers were also present in Bima district in January following massive protests against the exploration permit obtained by gold prospector Sumber Mineral Nusantara. 

A month earlier, three people were killed and 50 demonstrators were arrested when the police opened fire on the protesters, who had occupied a local ferry port for days. The incident led to an even bigger protest in January, with residents setting fire to the district office and forcing prison wardens to release some 50 detainees. 

Mulyadin, a spokesman for the protesters, said Densus 88 officers in Bima’s Lambu subdistrict searched people’s homes for escaped detainees and tried to blend in with ordinary officers so they would go unnoticed. 

However, National Police spokesman Insp. Gen. Saud Usman Nasution, formerly part of Densus 88 himself, denied that counterterrorism officers were present in Bima. 

“Why would they [be there]?” he said. “They are counterterrorism officers, and the case is a general crime. 

“I know [Densus 88] officers are well trained, but that doesn’t mean provincial police can just ask for their assistance,” he added. “Densus is under the direct command of the National Police chief.” 

Still, he confirmed Densus officers were in Papua to help the local police fight armed militias, and he justified their presence 

“Terrorism is not only limited to radicals waging jihad,” he said. “By the definition set under the 2003 Terrorism Law, terrorism refers to any act that can cause unrest.” 

But Noor Huda Ismail, an analyst on terrorism and security with the Institute for International Peacebuilding, said Densus 88 should stay away from handling separatism cases. 

“Densus was formed to tackle terrorism issues, and after all these years the [terrorism] network [in Indonesia] has not been uncovered completely,” he said. 

Ismail argued that terrorism suspect Umar Patek lived secretly in Indonesia after years on the run abroad, giving him plenty of time to expand his network here. There are also new players, he said, including the slain Sigit Qurdowi, who led a terrorist group that launched two suicide bomb attacks in Java last year. 

“There are also members of the Aceh camp who have not been captured to this day,” he added, referring to a terrorism paramilitary camp that the police raided in 2010. 

Taufik of security think tank YPP said that after Densus 88 formed, its officers tortured nearly all arrested terrorism suspects, with some suspects reportedly burned and beaten. 

“It was not until 2008, when they [the officers] got help from reformed militants and sources, that the torture stopped,” he said. “Armed with enough information about the terrorism network in Indonesia, [Densus 88] felt that there was no longer the need to extract information by torture. 

“But extrajudicial killings of suspected terrorists have continued,” he added. 

In 2010, Densus 88 officers gunned down five people in Cawang, East Jakarta, claiming they were armed terrorists who had tried to attack arresting officers. The police only ever identified four of the fatalities, fueling suspicions that the fifth victim had been innocent. 

“There is a great chance that suspects will be tortured again if [Densus 88] is allowed to engage in non-terrorism issues,” Taufik said. “They don’t have the knowledge [to investigate], but they’re under strong pressure to get the job done.” 

Yonias Siahaya, 58, knows this too well. In January 2010, he was crippled from the waist-down for two weeks after he was taken to the former Densus 88 headquarters in Tantuwi, Ambon. He had been accused of possessing a Benang Raja flag inherited from his father, an RMS militiaman. 

“My face was covered with a black plastic bag by four [Densus 88] officers,” he told the Globe at his wooden home in Ambon. “I was interrogated and they beat me in the chest whenever I gave the wrong answer. I collapsed down to the floor and that’s when they kicked me repeatedly.” 

He said the torture damaged some of his nerves and dislocated joints in his waist, but the police said he was faking his condition. He was forced to wait one and a half months before eventually receiving treatment at a state hospital in Kudamati, Ambon, although he was handcuffed to his bed the entire time.

“It still hurts whenever I go to the bathroom,” he said. “At night I often have migraine attacks.” 

Yonias now limps his way around after only partially regaining control of his leg muscles. He had to stop working as a construction laborer and now sells snacks and drinks from a rickety food stall. 

Charlotta Sapakoly, a widow of RMS activist Yusuf Sapakoly, said she noticed that the police crackdown on pro-independence activists in Maluku became more violent after Densus 88 got involved. 

“My husband was first arrested in 2003 for participating in an RMS flag-raising ceremony,” she said. “They didn’t torture him or anything then. But when he was arrested by Densus in 2007, it was another story. 

“On some days when I visited him in prison, he could barely walk — there were bruises all over his body. Once, I even spotted that there was a bone sticking out of his elbow. [Yusuf] wouldn’t tell me what happened. It was later, after he died, that one of his former cellmates told me what had happened.” 

A blow to the stomach had ruptured Yusuf’s kidney. 

“In September [2007], he was in a coma for three days,” Charlotta said. “His face was black and blue, and he had to have dialysis treatment 11 times.” 

Yusuf, detained for his involvement in the Benang Raja flag incident during Yudhoyono’s visit to Ambon in 2007, died in 2010. He never received proper treatment for the years of kidney failure and internal bleeding he sustained during his detention. 

Signs of harsh tactics surfaced again in August when Densus 88 joined the local police in Nafri, Papua, to investigate the shooting of a public minivan. 

The Institute for Policy Research and Advocacy (Elsam) said 15 people were arrested after the police stormed the Horas Skyline village; some people were kicked, beaten and threatened with pointed guns. The police later released all but two suspects for lack of evidence. 

“Among the arrested were under-age girls, identified as 8-year-old Desi Kogoya and 7-year-old Novi Kogoya, who were arbitrarily detained and endured inhumane treatments,” the rights group said in its year-end report. 

Haris Azhar, the chairman of the Commission for Missing Persons and Victims of Violence (Kontras), said Densus 88’s involvement in cracking down on pro-independence political activists threatens freedom of speech. 

“There’s the precedent that Densus 88 was involved in the torture of the peaceful separatist movement of RMS, which posed no physical threats to the public at large,” he said. “This is dangerous. If Densus 88 is allowed to handle non-terrorism issues, then all political activists will be treated as terrorists.” 

Haris said that by labeling political activists and separatist insurgence groups as terrorists, the Indonesian government also risks jeopardizing its prospects for peaceful reconciliation with pro-independence groups. 

“Densus 88 only sees its targets as enemies, not as discussion partners, which is how the government should view separatist groups,” he said. 

Elaine Pearson, the deputy director of Human Rights Watch’s Asia division, said she was deeply troubled by Densus 88’s involvement in suppressing peaceful protests. 

“There is a long history of counterterrorism forces in Papua conflating nonviolent political expression with criminal activity, and arresting political activists on dubious treason charges,” she said. 

“Densus 88 has an appalling human rights record, and without serious government oversight and with continued restrictions on access to Papua, any abuses by the force are likely to go unchecked,” she added. 

Australian Embassy spokesman Ray Marcelo, reiterating Canberra’s recognition of Indonesia’s territorial integrity, said his country does not support Densus 88’s involvement in non-terrorism activities. 

“The sole focus of Australian engagement with Densus 88 is in combating terrorism,” he said. “Australia does not provide any support to Densus 88 or any other unit of the [Indonesian Police] and [Indonesian Military] in relation to any activities directed at combating separatist groups.” 

But Saud said Densus 88’s authority to engage in separatism is outlined in the definition of terrorism as stipulated under the 2003 Terrorism Law.