At the base of the verdant mountains of Sentani, where dense, tropical jungle overlooks a sprawling teal lake, worshippers stream into church, men in suits and ties and sandals or batik shirts, women with colourful woven bags strung from their foreheads and slung over their backs.

Grey clouds hang low over the house of worship, a wood and tin shed with concrete floors and large open windows that let in the thick humid air.

Almost two weeks after a series of violent protests hit Indonesia’s easternmost territory, touching off the worst unrest in more than a decade, the pews in the majority Christian province are full and the parishioners are angry.

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The ring of evangelical hymns gives way to the rousing words of Rev Benny Giay, one of Papua’s staunchest supporters of self-determination. His fury is palpable.

“They called us animals!” he rails from the pulpit as women in the pews before him click their tongues in disgust. “Now there are anti-racist protests all over. It is like an earthquake!”

Ignited by malicious racial slurs two weeks ago, the protests in West Papua have spread and intensified, with thousands taking to the streets in a series of rolling and in some cases violent demonstrations.

On Thursday angry demonstrators torched parliament and police buildings in Jayapura. Police fired tear gas and six hundred extra paramilitary troops have been deployed to the city. At least six people have been killed as the volatile situation, unfolding in a region for decades roiled by separatist conflict, escalates daily.

The Guardian travelled to West Papua, obtaining rare access to the province’s leading pro-independence figures at a pivotal moment for the province. On the ground there was seething anger and resentment, but also hope that the rage on the streets will transform into real momentum for independence.

“The protests are a spontaneous action against racism,” says Victor Yeimo, from the West Papua National Committee, which advocates a non-violent struggle to achieve self-determination. “But what people want is freedom.”

Facebook Twitter Pinterest Victor Yeimo, from the West Papua National Committee. Photograph: Kate Lamb/The Guardian

‘A new time has come’

West Papua occupies the western half of New Guinea island, Indonesia’s most remote and least developed territory, almost the size of Spain. Lying more than 4,000km from the Indonesian capital Jakarta is home to some of the largest tracts of rainforest after the Amazon, and a bounty of gold, copper, timber and natural gas.

But the region is riven by deep divisions. The protests that began in early August were sparked by a viral video that showed Indonesian military officers taunting Papuan students in the Javanese city of Surabaya, calling them “monkeys”, “pigs” and “dogs”.

They have since spread to almost 30 cities inside and outside West Papua. There, demonstrators have flown the banned Morning Star flag, a symbol of Papuan independence, and held signs reading: “Papua merdeka, itu yang monyet inginkan,” – “Free Papua, this is what the monkeys want.”

After a market and government building were torched, the government in Jakarta sent more than 1,000 security personnel into the already heavily militarised province, sparking fears the protests would be put down with force.

But they have continued, spreading to Jayapura and the remote highlands, where thousands of Papuans in traditional dress carrying sticks, bows and arrows rallied to express their indignation.

Amid the unrest, key figures in the independence movement have seized on the momentum.

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Describing the situation as a “crisis of history”, Giay urged parishioners in church to educate their children so they could “become like Moses”, leading their people out of slavery.

“It’s like a new time has come and we have to reposition ourselves,” Giay told the Guardian after the sermon, as churchgoers walked back up the mountain, well-thumbed Bibles in hand.

‘We have never had a choice’

For indigenous Papuans, the demonstrations that began as a fight against racism have ignited decades of anger that date back to colonialism.

While Indonesia and its resource-rich spice islands were granted independence from the Netherlands in 1949, West Papua, then known as West Irian, remained under Dutch control until Indonesian troops parachuted in to “liberate” it in 1962. By August that year the territory was temporarily bought under Indonesian control.

In 1969, the controversial Act of Free Choice, a vote to enable the inhabitants of West Irian to determine their own future, was held. Many Papuans claim it was conducted under duress. Of a population of 800,000 people, some 1,022 Papuans, reportedly hand-picked by Jakarta and kept under military supervision, unanimously voted for integration.

Despite concerns over the process, the United Nations noted the results in Resolution No. 2504, without explicitly endorsing them.

Facebook Twitter Pinterest People flee as the local market is seen burning during a protest in Fakfak, Papua province, on 21 August. Photograph: Beawiharta/AP

In the minds of West Papua’s pro-independence leaders the sense of disenfranchisement that characterised the Act of Free Choice has lingered in the Papuan psyche, fuelling a sense of injustice and perpetuating an independence movement that refuses to go away.

‘Papuans want freedom’

Across the Papuan capital, Jayapura, storefronts are adorned with red and white, the colours of the Indonesian flag, decorations from Indonesian independence day celebrations on 17 August. But deep-seated nationalism is hard to find.

“Indonesian nationalism is only a symbol in Papua, a symbol that is forced upon us,” scoffs Victor Yeimo, “How can we say we are part of Indonesia when we have never had a choice?”

Filep Karma, a prominent independence figure who spent eleven years in jail for flying the banned Morning Star flag, sits on the balcony of his Jayapura home, wearing a camel safari suit, and an East Timorese flag on his cap. The independence symbols, he says, are “his motivations”.

“Sometimes in town the military threatens me and says ‘take off that pin’,” he says of his Morning Star flag badge, “I tell them, ‘shoot me first, then you can take it off,” he says with a laugh.

For years Karma says he has warned the Indonesian government about its racism problem, an issue that many Papuans know all to well.

Facebook Twitter Pinterest Prominent independence figure Filep Karma. Photograph: Kate Lamb/The Guardian

As a student in Java, Karma recalls a female friend who was a good singer cracking a joke in front of their friends. If they ever married, she jibed, “all the monkeys [Papuans] would know how to sing”.

“It hit me in the heart,” says Karma, from the balcony of his Jayapura home. “In church we would say we were brothers, so how could anyone say that?”

In Indonesia the general view of Papuans, he says, is “people with black skin, curly hair, and hairy bodies” who are “stupid, stinky and criminal”. Encountering it on a daily basis, he added, “gets to you psychologically”.

Around Jayapura, banners have been strung up calling for people to reject all forms of racism, but other ethnic divisions are plainly visible.

At the Jayapura Mall, almost all patrons and salespeople are noticeably non-Papuan. The indigenous Papuans can be found clustered outside in the heat, selling betel nut and woven bags on the pavement.

Papua is a land rich in natural resources, but the indigenous population complain they have not benefited enough from their natural wealth – across the country Papua has the highest rates of illiteracy and HIV.

President Joko Widodo, or “Jokowi”, has worked hard to develop Papua, regularly visiting and initiating new infrastructure projects. But there have been bitter disappointments too.

In 2014 Jokowi promised to solve egregious cases of human rights abuses, but critics say nothing has changed and for many Papuans, getting justice is more important than a new bridge or road.

“The government needs a humanitarian approach, not a military one if they want to win the hearts of Papuans,” remarked Marinus Yaung, a lecturer in international relations Cendrawasih University in Jayapura.

On the ground the issue of a referendum on self-determination is a sensitive one to for Papuans, who worry there could be repercussions for what they say.

At a traditional market one woman answered carefully. “Papuans are happy with Jokowi,” she said, “But it should be our right to choose.”

One local journalist who asked not to be named told the Guardian: “If you ask Papuans if they want freedom, they do.”

Even as the anger in Papua boils over, analysts say it is hard to see how much could change without significant international pressure and support – something that has been lacking for decades and shows little sign of materialising now.

To Jakarta’s elite, which vehemently maintains Papua is a legitimate and non-negotiable part of Indonesia, independence for West Papua remains a fanciful suggestion.On Thursday, chief security minister Wiranto said the government would not entertain any demand for an independence vote, according to Kompas.com.

“Demands for referendum I think must not be mentioned. Why? Because the unity of the Republic of Indonesia is final,” Wiranto said.

Karma is used to Jakarta’s intransigence and is realistic about Papuan dreams of independence:“Papua belongs to them, but in our minds it is ours.”