Tom Hyland – His childhood was spent in the jungle, where his family had fled an invading army. By the age of 11 he was leading a unit of independence guerrillas. He endured a decade in Indonesian prisons where he celebrated the fall of President Suharto with Jose "Xanana" Gusmao. In a miraculous escape, he fled to Australia a year ago today, on the plane that brought Bishop Carlos Belo to safety.

Jacob Rumbiak has a story to tell, one that in many ways defies belief. He is a West Papuan, born in 1958 in the village of Ayamaru, in Sorong district, in the Bird's Head area of the territory that is still officially known as Irian Jaya. His story reflects the recent history of his homeland.

When he was born, the vast western half of New Guinea island was under the control of the Netherlands, which had refused to surrender it in 1949 when the rest of the Dutch East Indies won independence as Indonesia. The Dutch, keen to maintain a foothold in the region, were preparing West Papua for independence. At the same time, President Sukarno was keen to "regain" West Papua in line with the Indonesian nationalist dream of uniting the entire former colony from Sabang, in Aceh in the far west, to Merauke, in West Papua in the east.

By the time Rumbiak was three, Indonesian troops were infiltrating West Papua. They claimed to come as liberators but many behaved as conquerors. Resistance grew. Encouraged by the Dutch, the West Papuans had declared independence on December 1, 1961.

To escape the Indonesian troops, Rumbiak's family (his father was a Protestant pastor and teacher; his mother a teacher) fled to the highlands. "In the jungle, conditions were bad. The enemy was not only the Indonesian military, but also malaria," Rumbiak says.

By the age of six he was carrying water and providing food for the guerrillas. Later he was used to spy on army positions. "The army thought we were just little boys, children, not the enemy."

At 11, he was appointed commander of a guerrilla company armed with arrows and a few rusty rifles, relics from World War II. "It was hard for a boy to give orders to men ... We fought for defence and survival, not for attack. In the jungle, sometimes we would move all the time. People would leave food for us. Sometimes we would stay in one place for two days. A long time would be a week, then we would hear of a military operation so we would move again."

One of his worst ordeals was when the army closely pursued his unit for five days and nights. They had no food or water. He has two bullet wounds on his right thigh, reminders of one close encounter, and another bullet wound on his left knee.

In pursuit of his campaign to wrest control of the territory, Sukarno had Soviet support. The Cold War was at its height and the United States, alarmed at Moscow's influence, pressured the Netherlands to reach a settlement. A 1961 agreement signed in New York by Indonesia and the Netherlands (the West Papuans were not consulted) handed control of West Papua to an interim United Nations administration and then to Jakarta for a further six years, when the people would decide their future in an "act of free choice".

In one of the great diplomatic frauds of the 20th century, about 1000 "representatives", hand-picked by Jakarta, "voted" to join Indonesia in a series of votes between July and August, 1969. With bitter humor, West Papuans refer to the "act free of choice" and the "act of no choice".

Rumbiak and his family moved in and out of the jungle until 1977, as Indonesian efforts to win over the West Papuans alternated between persuasion and repression – a pattern that has continued.

In 1977, as part of the persuasion policy, the government sent Rumbiak to high school in West Java. He went on to obtain degrees in mathematics and geography in Bandung, where he later taught. While in Bandung, Rumbiak played for the national soccer team, striking the winning goal for Indonesia in the Asia Championship Cup in 1984.

By 1987, Rumbiak was back in West Papua, lecturing in geography at Cendrawasih University in the capital, Jayapura. It was a time of intense nationalist foment. In December 1988, to commemorate the anniversary of the 1961 declaration of independence, the scholar and nationalist Dr Thomas Wainggai again proclaimed independence at a ceremony at which the Papuan Morning Star flag was raised in the main sports stadium. Wainggai was sentenced to 20 years jail and died in prison.

In December 1989, Jayapura was again in upheaval. On December 7, Rumbiak made a speech to his students, urging them to to carry on the struggle for independence peacefully. Warned that his name was on a list of nationalist leaders to be kidnapped and killed, he and three companions sought refuge in the Papua New Guinea consulate.

"I went there first for protection, but also to attract international attention. I hoped for international pressure on Jakarta to enter a dialogue with the West Papuans," Rumbiak says.

An extraordinary 15-day stand-off ensued, with Rumbiak and his companions resisting pressure to leave or cross the border into PNG. PNG Prime Minister Rabbie Namaliu sent an envoy to urge them to abandon the consulate. In Jakarta, Foreign Minister Ali Alatas told the foreign press he was trying to persuade the men to leave "on the understanding that they were not being pursued and there will be no action taken against them".

What wasn't disclosed at the time, according to Rumbiak, was the level of pressure applied. On Christmas Eve, 1989, Alatas, the then defence minister, Benny Murdani, and the armed forces chief, General Try Sutrisno, travelled to Jayapura to deliver a Christmas hamper to the activists and, as Rumbiak puts it, "to try to correct my false thinking". He laughs as he tells the story. "It was a big basket of wine, beer, biscuits, cigarettes, soft drinks, Christmas candles, clothes."

Rumbiak feared that crossing into PNG would end options for negotiations with Jakarta while severing his links with students and young people who regarded him as a leader, but eventually they left the consulate, with the promise they could safely return home. But with persuasion having failed, repression was now applied. He was arrested, tortured, and ultimately tried and sentenced to 17 years in jail for provocation and subversion. He served nine years and eight months. His companions got 12 years.

The list of the detention centres and jails in which he was held traces the air routes from eastern Indonesia to the capital – Jayapura, Biak, Morotai, Ujung Pandang, and on to Surabaya, Tangerang and Jakarta in Java.

He was tortured to repudiate his nationalist views and inform on other independence activists. "They put me in a special room, with a metal floor. They threw water on the floor and then switched on the electricity. It was very strong and I was thrown against the wall."

Twice he was told he would be killed. Once, he was trussed up in a military Hercules aircraft. The rear ramp was lowered in mid-flight and he was told he would be thrown out. He sang a spiritual song and the soldiers relented. Another time he was told he would be shot.

Rumbiak tells the story: "I said give me time to pray to my Lord. If you kill my body, you won't kill my soul. I will move from my body and I will wait for you. My soul will pray for you. Jesus loves you and I love you, too, because you don't know what you are doing, because you are following the command of your leaders. But one time the Lord will ask what did you do in the world for human rights." He laughs. "And you know, they're confused when I talked like this. And they lowered their guns and two soldiers, they cried."

Rumbiak spent four years in Kalisosok prison in Surabaya, where he studied for his third degree, in theology. In 1995, he was moved to Tangerang prison and kept in isolation in a stone tower for two years and four months. It was the worse period of his ordeal. "I was sick, very sick. I had no exercise, no sun. I could not walk."

In October 1997, he was sent to Cipinang jail in Jakarta, home to the most important political prisoners, which Rumbiak describes as a "first-class Javanese jail". His companions in Block 2A included East Timorese leader "Xanana" Gusmao. Gusmao appointed Rumbiak "coordinator of the garden" and he grew vegetables, kept a fish pond and raised chickens and rabbits. "We changed the jail's dry and suffocating atmosphere into a pleasant and peaceful environment," Rumbiak wrote in the foreword to Gusmao's autobiography. In May 1988, on a day of joy, hope and apprehension, the prisoners in Block 2A feasted on the produce of Rumbiak's garden and toasted the fall of Suharto with rice wine.

In August 1998, Suharto's successor, President B.J. Habibie, released Rumbiak into house arrest in Jakarta. Despite restrictions on his movements, he immediately returned to West Papuan affairs, travelling twice to Jayapura and once to Japan.

In August last year, in an act that seems both foolhardly and courageous, he flew to East Timor on an Indonesian military aircraft with the unsung heroes of last year's independence referendum – Indonesian students and democracy activists accredited as UN monitors. In the anarchy let loose by the Indonesian army after the vote for independence, militiamen attacked and burned the car he was in. He reached Baucau and sheltered in the UN police compound as it came under fire from Indonesian troops. "I thought this was the end, we were finished." He doesn't laugh when he tells this story.

On September 7, an RAAF evacuation Hercules arrived. Indonesian soldiers checked all going aboard. Bishop Belo, forced to flee Dili after his house was destroyed, had someone else's passport. The army tried to stop him but militiamen ("they had a heart", says Rumbiak) pushed him through the check point. Rumbiak, who had no passport, pretended not to speak Indonesian, saying he was from PNG. He said his passport was with the chief of immigration in Dili, a city now in flames, "and they believed me". This time he laughs. In February he was granted an Australian protection visa.

There are signs that the West Papua saga is entering a perilous and unpredictable chapter. In May and June this year, a congress of West Papuan representatives in Jayapura re-affirmed the 1961 declaration of independence. President Wahid has made conciliatory gestures – the persuasive policy – allowing the Morning Star flag to be flown and the territory to call itself West Papua.

But the repressive policy is being applied as well, with or without Wahid's approval. In an ominous development, pro-and anti-independence militia groups have been formed, while shadowy figures linked to the old Suharto regime funding both sides. Extra troops, including the notorious Kopassus special forces, have been sent in. All the signs point to a "special operation" with all the danger and duplicity that involves.

Yet Rumbiak remains confident. Freedom is inevitable, he says, if the people unite and remain disciplined. Despite, or because of , all he has endured, he believes freedom will be won through dialogue, persuasion, argument and logic. He has faith in those who back democracy in Indonesia and who want their country to regain its self-esteem. "I want this for Indonesia's dignity and I want this for West Papua, Melanesian dignity, too. Both sides will win, when West Papua wins its independence."

Rumbiak has learnt about realpolitik the hard way. You tell him that Jakarta will never let West Papua go; that the UN recognises Indonesian control; that the United States and Australia have gone out of their way to reassure Jakarta they recognise its sovereignty; that the West Papuans are being swamped by Indonesian settlers and will soon be a minority in their own country; that the obstacles are so many. He acknowledges all this, and says: "Ah, but they said the same about East Timor."

[Tom Hyland is The Age's foreign editor.]