It’s 35 years since Agapitus Kiku decided he didn’t want a future without freedom.

As a young man he’d been pressed into a work gang, bristling under the watch of Indonesian soldiers whose authority over his tribal country, in the south-east corner of the vast contested province then called Irian Jaya, he refused to recognise.

He saw no prospects for finding the work he wanted in forestry or mining. Those jobs went to soldiers, he says, or to the Javanese settlers pouring in through the transmigration program which the Dutch administration had begun and the Indonesians continued.

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In February 1984, an uprising by Melanesian nationalists in the provincial capital of Jayapura ignited months of brutal retaliations. Kiku, his wife, and their two small children started walking toward the Papua New Guinea border. So did most of their village and some 11,000 other Papuans, trekking on foot or navigating the coast in outrigger canoes - a seismic exodus of political protest that continued over nearly 18 months, triggering deployments of UN aid workers and international journalists, and upsetting regional sensitivities. Indonesia was not to be messed with.

Kiku’s family walked for a week, hiding at night from the soldiers. One child, aged two, died along the way. They crossed the Fly River where its wandering course bulges through the colonial cartographer’s best effort to carve up the island of New Guinea with a neat vertical rule. Here, in the middle of nowhere, the refugees declared they would not go home until they had “merdeka” - a word heavy with the promise of liberation, independence, freedom.

And still they wait, separated from their homeland by the wide, brown, infamously despoiled river that has served as the drain for the toxic sludge of the Ok Tedi mine for as long as they’ve been here. The more formidable and baffling barriers are the ones they can’t see, but which continue to mire the cause of West Papuan independence 50 years after the malodorous “Act of Free Choice” delivered the province to Indonesia.

‘They have their own agenda – freedom’

At last count, in 2014, the number of people living in refugee villages along the Fly was 5,500. A PNG immigration official who has lately been on the ground, part of a government team collecting registrations for long-awaited citizenship, suspects the population may be closer to 7,000. These are the hard-core stayers from within the 1984 movement, most of them from the Muyu tribe whose customary land straddles both sides of the border, plus their children and grandchildren.

They dug in when others drifted back, and refused relocation to the United Nations refugee agency’s settlement situated – diplomatically, and invisibly – well inland from the border.

“When I was with UNHCR we tried our best to pull them out of the villages to go to East Awin [settlement],” recalls Robin Moken, himself a Muyu man and former official in the provincial capital of Kiunga. “They said ‘no, we are fighting for our rights, and we stay here’. They remain there, they have their own agenda – freedom.”

For this they’ve paid a high price, forfeiting powerful inducements like recognition, schools and health care.

Facebook Twitter Pinterest West Papuan refugees rely on the notoriously polluted Fly River for food. Photograph: Jo Chandler/The Guardian

Kiku, now a wiry 68-year-old, secures our dinghy to the muddy bank below his village and brokers introductions to the people emerging, curious, from a cluster of stilt huts and the surrounding bush.

The past few months have been anxious ones for the West Papuan diaspora. Despite media constraints including internet blackouts, horrific stories float over the river as another violent eruption of independence activism and retaliation plays out. There are questions around what that might mean along this wild, porous frontier, and how those ructions might be felt more widely.

UNHCR and UNDP representatives have recently visited Kiunga, reportedly working with local authorities and refugee representatives on their preparedness to receive a new wave, though neither agency would confirm these reports.

Western Province Bishop Giles Cotes has confirmed that 13 families have reportedly crossed the Fly River north west of Kiunga. There is a committee forming to organise care for those who come across.

‘We don’t want to fight’

To smooth the way in exploring these delicate issues, our delegation to two refugee villages also enlists a guerrilla veteran of the ‘70s jungle struggle and two next generation activists.

One of them, Toni Sapioper, like Kiku, was part of the 1984 wave, though he was just three when his mother smuggled him and his six siblings across the sea border from Jayapura into Vanimo. He grew up in East Awin settlement and proudly claims lineage as a nephew of the late Seth Rumkorem, a founding leader of the Free Papua Movement (Organisasi Papua Merdeka, or OPM), who proclaimed the Republic of West Papua in 1971.

The villages remain OPM strongholds. Refugee communities have two fervent articles of faith – independence, and Catholicism.

Damianus Warip, 62, is at church with most of the other elders praying the rosary when we arrive. Another veteran of the jungle conflict says he worries that the escalation in clashes on “the other side” will bring more Indonesian military to the border. He crossed the river in 1983, ahead of the main wave, determined “to stay and to fight for merdeka”. That refrain punctuates his answers to every question: “The only thing is merdeka, the only thing”. But it must be realised peacefully, he says. Through a translator, he asks that “Indonesia hear our peaceful demands … we don’t want to fight against Indonesia”.

In the next village, another grey-haired warrior who today himself as the region’s OPM commander-in-chief is more belligerent. In an hour-long, impassioned oration to a closely attending audience of younger men he speaks of how he wants West Papuans over the border to rise up again this 1 December, urging them to “come and join, because this is our opportunity to rise to our destination, our idea … what we want is international community support when we do this, like [Timor Leste]”.

“We want everyone to arise,” he says, adding his people are “out of patience” and have suffered enough.

Refugees on their own land

The sufferings of West Papuans over the border are often hard to know due to the lack of access for outsiders, including media, though the glimpses that break through are horrifying. On this side, remoteness and disinterest cloak the less dramatic, grinding hardships of displacement, compounded by layers of cruel luck and circumstance.

The combination of vast distances, lack of infrastructure and corrupted budgets mean health services are shatteringly scarce across PNG, and in Western Province, they are worse than even the national average. For decades, Fly River refugees have relied almost entirely on basic health patrols by nuns from the Catholic missions. There’s a lot of sickness – malaria, tuberculosis, elephantiasis, chronic malnutrition, says a village leader, Robert Maun. In his community two teachers instruct more than 100 elementary students divided into four classes.

Facebook Twitter Pinterest Januarius Anton, 30, teaches 57 students in a single room class with a broken floor and just a half a dozen old desks. He says he has not been paid for 10 years, and survives on the support of the community. Photograph: Jo Chandler/The Guardian

Most of the refugees share customary ties with their PNG kin, seeing themselves as refugees on their own land. Both communities struggle for the basics of food and water in a climate-changed landscape with ever fiercer extremes of heat and wet and dry. The mission-supplied water tanks in one village are empty, and with the river too toxic to drink and cook, hauling water long distances in 20 and 50 litre containers becomes a consuming ritual.

The staple food, sago, is in short supply. The sago trees along the river all died in 1998, for which they blame Ok Tedi. Maun says sago poisoning killed a family of five in his village three years ago. Fish are the lifeline of the local communities, providing food and income at the Kiunga market, but “sometimes we see the sores on the fish, we throw them back”, explains fisherman Andrianus Kundimoko. “If no sores, ok, and we eat or sell them.”

“The river corridors are dying,” says Robin Moken. The bountiful Fly of his memory is long gone. “If rain comes, it’s OK. But if no rain … they are drinking from that no-good water. If you want to make sago, sago is washed in the river … you can clean it, but it’s very dangerous.”

While landowners on the PNG side of the Fly River receive compensation payments for the damage done to their river, those born on the western bank qualify for none of it.

“Apart from the struggle for their freedom is the impact from the pollution in the river system,” says Moken, who was instrumental in landowner legal action against BHP. There was talk for a time about trying to recognise West Papuans landowners in the payments, he says, but then there were concerns that the Indonesian Government “might think that we are aiding the rebels”. So that notion died.

A new generation of fighters

In the villages, the words of ageing warriors provide a glimpse of the tensions that have long distracted and derailed their movement’s ambitions. Back in the lively refugee corners of Kiunga, another dimension comes into play, one that will define where it goes in the future – the generational shift.

Here the children of the 1984 exodus – largely those hailing from East Awin, who had an education denied the children in the river camps – are preoccupied with learning what is playing out over the border, finding opportunities for leveraging diplomacy and enlisting international human rights law. They do so within a climate of ever-present watchfulness.

Facebook Twitter Pinterest Esther Rumsowek (right), a high school teacher and Esther Kurni, 71, the mother of Toni Sapioper, who fled Jayapura with her seven children by outrigger canoe in 1984 after her home was surrounded by Indonesian soldiers. Photograph: Jo Chandler/The Guardian

“Here, we cannot talk in public, because we are on the border area,” says Esther Rumsowek, 25, a high school teacher. That said, here they can wear the Morning Star on their chests and post it on their social media, “but if they caught you on the other side, that is the end of your life”.

While the women hover at the margins of the political gatherings in the village, in Kiunga they are front and centre.

Herminje Wakum, 31, is a primary school teacher and the daughter of the late John Wakum, one of the leaders who led refugees over the border into Vanimo in 1984. “It’s in our blood,” she says. “Whatever our parents did, they pass it on to us and our generation, we still continue so that we can achieve what they wanted.”

Toni Sapioper recalls that in his first years in PNG, he didn’t understand why the family had fled. “So I kept asking and asking my parents and they told me we came for this reason, only to free our motherland. I grew the same feelings, the same ideology.”

He’s not interested in militancy, he says, but in justice, and an undoing by the international community of what was done in 1969.

“That is why I am involved in the struggle, in order to carry on, for what they left behind.”