I'm walking down one of the main streets in Jayapura, with a foreign journalist pass around my neck and I don't think one of those has been issued in over a decade. To be honest, I'm more accustomed to creeping around here in secret. So it feels a little bizarre. But Indonesia says this place has changed. I've agreed to a condition or two. But otherwise I'm here to test that proposition. And we'll see how far I get.

I'm here as a guest of Franz Albert Joku and Nick Messet. For decades both of them were senior members of the outlawed independence movement. In a surprise move to their former comrades, they both returned from exile several years ago and since last year began working as advisors to the Politics and Security Ministry, spruiking Indonesia's message at various international forums. In that capacity, I met them a few months ago in a heated exchange at the Indonesian consulate in Sydney.

FRANZ ALBERT JOKU, FORMER INDEPENDENCE LEADER: But the world will not come to our aid Mark! You know that. We have to do it ourselves from within.

NICK MESSET, FORMER INDEPENDENCE LEADER: It's changed Mark.

REPORTER: Who can go there?

FRANZ ALBERT JOKU: You can come with me.

REPORTER: I can't go there.

FRANZ ALBERT JOKU: You can come with me on Monday if you want to. Can SBS get you a ticket and come with me on Monday?

REPORTER: They can get me a ticket...

FRANZ ALBERT JOKU: I will take you to Papua. 

That sparring ultimately led, to my surprise, to a visa.

REPORTER: Well, I don't know how you did it, but thank you.

FRANZ ALBERT JOKU: If people like us, considered a threat to the state of Indonesia, can become citizens again, I don't think it's so difficult bringing Mark Davis into Indonesia. As you can see, journalists are not banned but you go through the correct channels...

REPORTER: Come on Franz. No one has been here in 10 years so I'm very grateful.
 
FRANZ ALBERT JOKU: I know.

REPORTER: It's not normal. This is not normal.

FRANZ ALBERT JOKU: I mean, it's better to do it officially than to sneak in.

We're driving up to the border.

FRANZ ALBERT JOKU: Over here.

REPORTER: So, we have to talk to these guys?

It's a sensitive area but like getting a visa not too much of a problem for Joku and Messet.

FRANZ ALBERT JOKU (Translation): But we came by another road, I asked the police chief last night.

OFFICER (Translation): He gave you permission?

FRANZ ALBERT JOKU (Translation): Yes. 

OFFICER (Translation): So we'll go there together. Mr Eddy! Can you help us get there? I'll accompany them later.

FRANZ ALBERT JOKU (Translation): Thanks gentlemen.

REPORTER: That was the easiest roadblock I've ever faced in Indonesia.

This is normally a thriving market that straddles the border with Papua New Guinea. Locals from villages on both sides of the border are allowed to meet here to trade. But a recent shoot-out between police and the armed independence movement, the OPM, led Indonesia to shut the market. 

MAN (Translation): We heard gunfire and a lot of them came out.

The banned West Papuan flag was raised here - the most common act of rebellion in the province - and a fire fight broke out. One policeman injured and reportedly three Papuans killed.

MAN (Translation): I can't say... Maybe the police chief can answer.

OFFICER (Translation): He'll respond to everything later. That's his job. He will explain this incident.

In coming to this province, I made two specific pledges - that I wouldn't film or contact the armed resistance and that I would fairly represent Indonesia's position. What I didn't agree to was being constantly followed and filmed by seen and unseen forces. It's still extremely tense here but Franz Albert sticks to his word - to show me the places I want to see.

OFFICER (Translation): The shooting was from here on the left, shooting in that direction.

REPORTER: They come out of these mountains, huh?

FRANZ ALBERT JOKU: Yeah.

It was across this very border that both Messet and a young Franz Albert fled with his family during a wave of violence and killings in 1969.

REPORTER: Your father was severely beaten and his life was threatened and he had to leave?

FRANZ ALBERT JOKU: Even though it happened nearly five decades ago, I'd rather not talk about it because it's painful, like any Papuan will tell you. I want to look ahead and using the experience we have had before, to be able to take a position that will ensure the future wellbeing of my children, grandchildren and their children.

For decades, Franz Albert Joku was seen by many West Papuans as the future foreign affairs minister in an independent nation.

FRANZ ALBERT JOKU, WEST PAPUAN INDEPENDENCE LEADER: Successive Australian governments have been uncomfortable with the West Papuan independence struggle...

Living in Papua New Guinea, he returned in 2000 to attend the Papuan Presidium, the most significant West Papuan political meeting since Indonesia gained possession of the country in the 1960's. Chief Theys Eluay was elected leader with Franz Albert constantly at his side as foreign affairs spokesperson. The presidium was viewed by many as a serious threat to Indonesian rule. It led to an explosion of optimism in West Papua that political freedom, if not independence, was coming.

But the golden days were short lived. Chief Theys was murdered by Indonesian military officers, strangled and his body dumped by the road. The movement collapsed and Franz Albert rumoured to be next on the list fled to PNG.

FRANZ ALBERT JOKU:  You will not come to our aid, the United States will not sacrifice its interests...

They were bitter years and his resentment grew towards the nations that ignored his people's cause, as much as it did towards Indonesia.

REPORTER:   No one was interested. That's the truth.

FRANZ ALBERT JOKU:  That is correct. Australia was not interested. The United Nations was also half hearted about it in 1969. Why should I place my life and my future in the hands of such people? I'd rather deal with the only group of people that were interested in Papua, is the Indonesian leaders.

Today, Franz Albert and Nick are meeting with the police, as they often do, to discuss security issues in the city and province. 

FRANZ ALBERT JOKU: Mark, he got shot...

Lieutenant Colonel Alfred Paparai is the police chief for Jayapura City. He was shot in the leg at the recent conflict at the border.

FRANZ ALBERT JOKU:  As a former activist I must clear my name. I can't come here and hide in seclusion. I have to liaise with authorities here.

For many Papuans, Franz Albert liaises a little too much with authorities here but for him Indonesia is now the only relevant power to affect change in Papua.

FRANZ ALBERT JOKU:   Only time can tell whether I am a collaborator. I came back because my people are here. My land is here. Why should I be classified as collaborator? This is my land. And I'm proud whether I'm under the Indonesian Government or under the autonomous rule of Papuans ourselves, or whether it's independence - I must be here.

Off camera, Messet tells me that he still feels nervous coming into these headquarters. He was once tortured in this very building. It was while being beaten here with a gun barrel in his mouth that he decided to flee. And the place he escaped from was less than 100 metres down the road from the police station.

NICK MESSET:  I remember, yeah. We just leave from this area here, it's now a building. I was in the bush for one year with the OPM and I had to come out because of my family. They tried to arrest them so I have to come and we went together to seek political asylum in Papua New Guinea.

Messet spent most of the next 40 years in Sweden. Presumably he never dreamt he would be back here exchanging civilities with the head of police for the entire province. Inspector General Tito Karnavian trained with the AFP in Australia. Tito concedes atrocities have occurred in Papua but maintains that proper human rights are now accorded to all.

INSPECTOR GENERAL TITO KARNAVIAN:  We have got a lot of standard operating procedures and also ethical codes you know not to violate human rights. So the present day it's very much different from the police before 1998 when the police was being part of the armed forces.

It's a view echoed by Indonesia's Foreign Minister, Marty Natalegawa.

MARTY NATALEGAWA, INDONESIAN FOREIGN MINISTER:  It's very, very important to recognise that there is a sea change in Indonesia in terms of outlook on democracy, on human rights and whenever human rights violations occur in Papua, it's an exception to the rule and it's an aberration.

It's true that the attitude in Jakarta towards atrocities and abuses in Papua has changed. The question is has that message got through to the police, military and intelligence forces on the ground.

REPORTER:  This one?

DRIVER:  Yeah.

My first attempt to slip away from my hosts and the security cordon around me doesn't go well.

DRIVER (Translation):  There is someone following us. Yes, there is. Soldiers are following us.

I'm trying to escape to another town where more Papuans live, now they've been so effectively squeezed out of Jayapura.

REPORTER:  Is our friend still with us?

DRIVER:  Yeah. At the back of us.

A local contact is happy to give me a lift until he sees two motorbikes following our every turn.

REPORTER:  Still there? So this guy would be from police or army?

DRIVER:  Army.

The men on the bikes are soldiers, more commonly in plain clothes now than uniform. They are the secret army that rules West Papua. People are terrified of them.

REPORTER:  That's him?

DRIVER:  That's him. In the white helmet.

To put it bluntly, it would be highly unlikely that a policeman would kill you in West Papua today but these guys might.

REPORTER:  So he will stay there watching us until we go again? Yeah, he's watching us. He's watching us.

It's too risky for my friend to remain with me and he drops me in a nearby town where I find other means of transport. I make my way to a student recently bashed by police and now in hiding in fear of his life.

YALI (Translation):  They hit us with rifle butts and with their fists.

REPORTER:  Why?

Yali was organising a protest for 50 political prisoners who were locked up in Jayapura. When he and a friend approached the police to seek permission to cross a road, they were both seized and beaten in custody with staggering ferocity.

YALI (Translation): I also got electric shocks, and they strapped my feet with sharpened bamboo.

I put his case directly to the police chief.

INSPECTOR GENERAL TITO KARNAVIAN:  They are the first ones stoning the police, yeah? They are stoning the police and you've got some police officers being injured, then of course they had to disperse of them.

REPORTER:  The account that I heard... and perhaps I've heard the wrong account... 

INSPECTOR GENERAL TITO KARNAVIAN:  It is a crime, then the police...

REPORTER:  The account that I heard was that the stoning didn't happen until they had been arrested.

INSPECTOR GENERAL TITO KARNAVIAN:  No, no, no, no, that is of course their defence, right.

According to Yali, there was no stoning until after they were arrested. 

YALI (Translation):  When our friends behind us saw them doing this, they may have started panicking, so they ran back, got some rocks and started throwing them at the police.

Whichever account is true, Yali maintains the torture continued for more than 24 hours and both he and his friend were hospitalised.

INSPECTOR GENERAL TITO KARNAVIAN:  They are resisting to be captured and the police must paralyse them. The police must paralyse them with their bare hands, in that case, their bare hands, without any weapons.

It's not an easy province or situation to police. Some officers have died in these typical confrontations. But more often than not it's a Papuan. The cycle of demonstrations and severe police retaliations has become common in Papua. 

If protesters don't end up in hospital or a grave, they often end up here. I can't get in myself but I managed to smuggle a camera inside Jayapura prison to get footage of the political prisoners locked up there. Prisoners like Filep Karma.

FILEP KARMA, POLITICAL PRISONER (Translation):  I was jailed because I was fighting for...I was voicing the right of the Papua nation to be independent.

Karma was jailed in 2004 for holding this rally which included the flying of the banned West Papuan flag - a criminal offence of subversion. Karma was sentenced to 15 years. Dozens of others are in prison with him for similar offences and for expressing similar views.

FILEP KARMA (Translation):  Already many Papuans have been killed, persecuted, and that's been hidden by Indonesia until now. Their behaviour in the villages is cruel and violent. So if our friends overseas are slow to act, then the Papuan people may become extinct

Edison Waromi declared himself Prime Minister of West Papua after a vote at a rally in 2011. He was sent here the next day.

EDISON WAROMI (Translation):  As long as there are political prisoners in West Papua that means that democracy is being silenced.

Forkorus Yaboisembut met the same fate for organising the same 2011 rally.

FORKORUS (Translation):  We heard gunfire, everyone on the field panicked, some of them ran away and three people were shot.

DAUGHTER (Translation):  My father was detained because he was struggling to free Papua from the Republic of Indonesia.

Forkorus' daughter Olla has gathered a group of his father's friends, who were arrested with him and have since been released.

MAN 1 (Translation):  We have been killed, massacred, tortured. We have been robbed of our rights and riches.

I've taken measures to avoid being followed but all of these people are taking a risk in coming to see me.

MAN 2 (Translation):  At that time our friends...were shot dead.

For them it's a risk worth taking for the world to know what happened to them.

MAN 1 (Translation):  And we were also tortured. Here's proof. After the Congress, my eyeball was hanging out and I also have a scar here.

At a peaceful rally on a school sport field, Olla's father had summoned what he called the Third Papuan Congress as troops gathered ominously outside.

INSPECTOR GENERAL TITO KARNAVIAN:  There was a conference, an illegal conference, so it can be dismissed.

When Forkorus declared that West Papua was an independent nation, the response was immediate. The police are mostly in uniform. The head kickers in plain clothes and bike helmets are mostly soldiers and military intel. To human rights groups, this response to a totally peaceful rally is a prime example of Indonesian brutality. To Indonesia, it's a prime example of restraint.

INSPECTOR GENERAL TITO KARNAVIAN:  If they resist, then you can go for coercive methods to dismiss. These methods are being applied everywhere in police offices in the world.

Several officials point out to me that a decade or so ago this event could have turned into a massacre. As it was, three were shot dead on the spot. Three died in hospital. There were 12 fractured skulls, 300 arrests. That is some improvement.

FRANZ ALBERT JOKU:  Papua is no exception. We also have people killed on Java, we also have people killed in Aceh. This is Indonesia and not Australia.

REPORTER:  This is true.  It seems to me that Papua is more in a state of war than any other part of...

FRANZ ALBERT JOKU:  A lot of what you say is going on and as far as I'm concerned, and I say this publicly, they stand condemned because it is against humanity and justice. They stand condemned and I say it publicly, including the Government of Indonesia will see what I am saying.

INSPECTOR GENERAL TITO KARNAVIAN:  We ban our officials to use bullets - maximum if they are doing anarchic - rubber bullets - maximum. 

It's a positive sign that the police chief was confident enough to talk openly with me, but not so the Governor, theoretically the most senior official in the province. Governor Lukas Enembe refused a formal interview request and appeared mortified when I approached him at a Jayapura hotel, asking him to join a meeting to discuss currents politics in Papua.

GOVERNOR LUKAS ENEMBE: Indonesia is nice country. Beautiful people in Indonesia. We have everything in Indonesia.

Nearby, a group of prominent Papuans are gathering. Each of them are brave enough or high-profile enough to speak their minds, a rare commodity for Papuan civilians.

FRANZ ALBERT JOKU:  I often say human rights situation has actually improved. Otherwise we would not be sitting here discussing human rights with you. We would be stopped.

Three of the people here have appeared on leaked military hit lists in the past - outspoken church leaders, Socrates Yoman and Benny Giay.

BENNY GIAY, CHURCH LEADER:   In Papua, we know who is in control - it's the military and police.

And former secretary of the Papuan Presidium, Thaha Al-Hamid, together with businesswoman Mary Yoweni, I ask each of them whether things have improved in West Papua or not.

NICK MESSET:   Human rights abuses have drastically decreased.

REPORTER:   People are still being beaten if they protest?

NICK MESSET:   Well if it happened in Australia, if you break the law, you have to be punished too.

REPORTER:  Well, you don't have your skull cracked.

NICK MESSET:   This is different to Australia, Mark. This is Indonesia and we have to follow that.

SOCRATES YOMAN:   I'm a church leader, I'm telling you what is really happening here. Not getting better.

The differences in their perceptions of whether Indonesian attitudes to the province have changed soon become stark.

BENNY GIAY: But they use this Subversion law, they use this Subversion law, as a licence to kill Papuans and that's evil. That's evil.

NICK MESSET:  Well I don't agree.

BENNY GIAY:  No, no, I'm telling you...

MARY YOWENI:  Honestly, I'm in a different generation to all of the men sitting here.

Mary is herself a sign of change, a rich Papuan woman. She came here today to support the Indonesian Government and the opportunities it's given her. But as the argument unfolds about human rights, she struggles to maintain her composure.

MARY YOWENI:   I don't want to be a liar. I know I get blessing from God. I live here because God lets me live. Not because of anybody. So, something must be wrong, something must be wrong.

The debate goes on, but for Thaha Al-Hamid, the real problem is not here in Jayapura where the grip has loosened.

REPORTER:  Do you feel like you're a free man? Is your tongue free to talk?

THAHA AL-HAMID (Translation):  No, no, I'm okay, I'm all right. But don't ask me, I'm here in the city. Ask the people in the villages. That's the most important thing. Not me...Them!

It's in the remote mountain villages that the most horrific abuses have occurred and by most accounts are still occurring.

MOANA CARCASSES KALOSIL, VANUATU'S PRIME MINISTER:  I've come here to call for immediate action.

Just two months ago, Vanuatu's PM addressed the United Nations about four videos he had received from inside Papua. All of them were filmed in the last four years. All reveal atrocities at the hands of the army in search of rebels or their supposed supporters.

SOLDIER (Translation):  This guy's OPM, he's killed soldiers. 

All in such remote areas that the victims would have only a vague idea of what a city was, let alone what nationhood means.

SOLDIER (Translation):  Record this, mate. Record this. They are traitors. Bastards, you want to be independent?

None of them far from being first contact regions and this is their introduction to the world.

SOLDIER (Translation):  You going to shut up? I'll slash you.

MAN (Translation):  No. 

MAN (Translation): Papua.

Some of it is too disgusting to broadcast.

REPORTER:  Some of these reports are truly horrific. Do they concern you and is there any action being taken?

MARTY NATALEGAWA:  Yes, of course they concern us. But the difference now is there is no culture of impunity and where cases of human rights violations occur, the individuals concerned would be brought to justice. And there is a legal process under way.

In this case, which involved the most extreme acts of torture, three soldiers were charged with insubordination. They were not dismissed. 

Tito's police force is undoubtedly under better restraint than the army and yet still people are dying at their hands. A preacher in Benny Giay's church was recently shot and killed by the police and he wants to show me the photos.

BENNY GIAY:  This is the pastor...

REPORTER: The pastor, the reverend?

BENNY GIAY: Epinus, yeah.

Epinus Tabuni Magal was killed near the Freeport mine. The circumstances are murky as there is a tribal war going on there and the police are often in the middle of a wild battle.

REPORTER:  He went to help?

BENNY GIAY:  Yeah, this is the one.

Benny's witness claims that the preacher was shot in cold blood while trying to photograph the body of another victim. It's a claim the police deny. But Benny has another photo which is more surprising to me. Just two days before came news of a police shooting in a remote location.

REPORTER:  I heard this. This is yesterday or the day before yesterday? And this one, he's dead?

BENNY GIAY:  He's dead.

REPORTER:  They're not saying he's dead, though.

Investigating officers swore to me that only rubber bullets were used to disperse a rowdy crowd in keeping with current regulations.

BENNY GIAY:  They said they use rubber bullets?

REPORTER:  Rubber bullets, that's right. Rubber bullets.

And only light injuries ensued.

REPORTER:  Because I spoke to the police chief on this one.

BENNY GIAY:  No one died?

REPORTER:  That's what he said.

BENNY GIAY:  He said no one died?

REPORTER:  He did say that.

BENNY GIAY:  I think we live in a different world. Using different logics, different eyes, we use a different sense of reason.

Reporter/Camera
MARK DAVIS

Producer
DONALD CAMERON

Researcher
MELANIE MORRISON

Translations 
ROBYN FALLICK

Editor
WAYNE LOVE