HARLEY: Zamboanga, the Southern Philippines. On the face of it, just another provincial city in South East Asia - but this is a hunting ground. Terrorists come here to kill. It’s a volatile, unpredictable existence. Today the streets are quiet, tomorrow they could be like this. In recent years, attacks by local militants have left hundreds dead but they don’t work alone. Al Qaeda have been here - Indonesia’s Jemaah Islamiyah, JI, are certainly here.

In the war against terror in South East Asia this is the new frontline. Here in Zamboanga City and the islands to the south, Philippine military, police intelligence units and US special forces, are attempting to break the back once and for all of the international Jihadist networks that have operated here for the past decade. It won’t be easy and already they are paying a deadly price.

While the US forces here play a secretive high tech game and The Philippines military have the firepower, it is the police who are the public face in the war against terror.

COLONEL ANGELITO CASIMIRO: I am in the grasp here of terrorism.

HARLEY: Colonel Angelito Casimiro, known simply as “Lito” leads a police intelligence unit tasked with hunting down Islamic extremists.

COLONEL ANGELITO CASIMIRO: My fight with terrorism started when I was a young lieutenant and now that I am still in the service after 18 years, I even put my life and my family’s life on the line.

HARLEY: For the next ten days I will be privy to the frenetic workings of his team. It’s low tech, low budget counter-insurgency but they have an enviable success rate. Their adversaries, Islamic militants, grudgingly refer to the unit as the “Killing Machine”.

COLONEL ANGELITO CASIMIRO: These are members of the Abu Sayyaf Group or we call them the [INAUDIBLE] Islamiah.

HARLEY: The Abu Sayyaf, the ASG, is Lito’s primary enemy.

COLONEL ANGELITO CASIMIRO: The first person is Kadaffi Janjalani. He’s the leader of the Abu Sayyaf Group.

HARLEY: The Abu Sayyaf has recently strengthened its links with Jemaah Islamiyah.

COLONEL ANGELITO CASIMIRO: [Pointing to next man’s picture on "wanted" chart] He is the second man in command.

HARLEY: While the Abu Sayyaf provide sanctuary, JI bomb makers pass on their skills used to such devastating effect in Bali.

COLONEL ANGELITO CASIMIRO: Dulmatin is a member of Jemaah Islamiyah and they were the Bali bombers.

HARLEY: The Philippines has waged a long and complex war against Islamic extremists fighting for an independent homeland in the South. This group, the Moro Islamic Liberation Front, invited Indonesia’s Jemaah Islamiyah to train them in the mid 1990’s. Later, al Qaeda came trained by Fathur Rahman al-Ghozi in their own dedicated terrorist camp and adding to this menacing threat, local group Abu Sayyaf. Their speciality? Beheadings.

COLONEL ANGELITO CASIMIRO: Sometimes they will shift allegiance.

HARLEY: As Lito sees it, his enemy is constantly evolving. Allegiance is shifted and the names are changed but they all come from one big terrorist family.

COLONEL ANGELITO CASIMIRO: The terrorist group in The Philippines are umbilically connected to each other, the father being an old warrior of the modern National Liberation Front and the eldest son a member of the Moro Islamic Liberation Front and the youngest son could be a member of the Abu Sayyaf Group.

HARLEY: Whatever the allegiances, Zamboanga, Lito’s patch, remains a constant target.

COLONEL ANGELITO CASIMIRO: We just received this information from autonomous region, Muslim Mindanao that the City Mayor of Zamboanga is going to be kidnapped by the ASG. So tonight we’re going to do some disruption operation to disrupt whatever plans they would like to do in the City of Zamboanga.

HARLEY: The job of intercepting any terrorist activity falls on Lito’s Special Operations Group.

OPERATIONS OFFICER: Tonight we are going to conduct surveillance against a suspected JI member. We have been now on surveillance for almost three months already.

HARLEY: We are heading into a Muslim enclave of Zamboanga City. Tonight's target a key JI figure suspected of funding terrorist attacks.

OPERATIONS OFFICER: We should be discreet in our conduct in this surveillance so we will not be compromised. So we will be very much careful in doing this job.

HARLEY: This is no place for the faint hearted. Point blank shootouts are common, yet no one in the team has a bulletproof vest. Lito’s team has an informant on the ground, his name is Toy. As we near the target, the night’s operation starts to unravel. The crowds in the street signal something is amiss.

OPERATIONS OFFICER: What’s the problem here?

MAN IN CROWD: Someone was shot.

OPERATIONS OFFICER: Is he dead?

MAN IN CROWD: Yes, he’s dead.

OPERATIONS OFFICER: Who shot the guy?

HARLEY: The man killed is Lito’s informant Toy, gunned down just minutes earlier.

OPERATIONS OFFICER: Just right now?

MAN IN CROWD: Yes, just right now.

OPERATIONS OFFICER: Who shot? Were they on a motorcycle?

MAN IN CROWD: No, they were just walking.

OPERATIONS OFFICER: Was his gun taken?

MAN IN CROWD: Yes.

HARLEY: You’ve literally just found out that one of your agents has been killed?

OPERATIONS OFFICER: Yes. When we talked to [INAUDIBLE] just a while ago, they informed us that it was Toy who was gunned down.

HARLEY: Are you shocked?

OPERATIONS OFFICER: Yes.

HARLEY: So is that a serious loss to your surveillance capabilities?

OPERATIONS OFFICER: Yes because we lost one of our eyes and ears in the area. We’d better get out because they might suspect us.

HARLEY: Too many people... too many sets of eyes.

OPERATIONS OFFICER: Yes sir, that’s why we will not go on with our planned surveillance.

HARLEY: An hour’s ferry ride from Zamboanga brings you to Basilan Island and its major port, Isabala. It’s relatively peaceful now though four years ago the situation was very different. The Abu Sayyaf’s declared struggle for an Islamic State had degenerated into anarchy.

COLONEL ANGELITO CASIMIRO: The city was the birthplace of the Abu Sayyaf Group and we have to pour in a lot of manpower, logistics including military police to secure the city. People are being beheaded. People are being shot. And you would fear for your life when you’re in the city because anything goes and anything will blow up.

HARLEY: Despite assurances that Philippines' authorities have regained control here, Lito isn’t taking any chances. Extra bodyguards are picked up at the local police headquarters.

We’re still travelling with about six or seven armed police with us, are you being overcautious?

COLONEL ANGELITO CASIMIRO: You’re a foreigner and we would like you to be back with your family. We don’t like that anything happens to you so that’s the standard precaution whenever there are foreigners coming here.

HARLEY: Five years ago there were lots of foreigners here though not by choice. The Abu Sayyaf pulled of an audacious series of kidnappings, grabbing Americans, Europeans and Filipinos. Some were missionaries, others abducted from nearby holiday resorts.

Huge ransoms were demanded and the negotiations with extremists turned into a fiasco. Having trapped the senior Abu Sayyaf leaders and their hostages in a hospital, a number of military officers struck a deal with the terrorists and split the ransom money. The officers involved reportedly got one hundred thousand dollars - local politicians half a million, the Abu Sayyaf another half million. The Abu Sayyaf leadership was allowed to walk away from the hospital in broad daylight into the nearby jungle.

But the tables are now turning. These inmates are some of the alleged Abu Sayyaf kidnappers, captured two years ago, they are still awaiting trial. All the prisoners declare their innocence but police claim considerable success – more than two hundred Abu Sayyaf have now been convicted or detained but the ringleaders are still at large.

COLONEL ANGELITO CASIMIRO: These are just leg soldiers. The leadership are still in the mountains on the island of Sulu.

HARLEY: With Basilan relatively secure, the focus has now shifted to the island of Sulu, an hour’s flight south from Zamboanga. Sulu holds dark memories for the Colonel and within twenty-four hours, old wounds will be reopened.

This has become the new terrorist heartland in the Southern Philippines – the Abu Sayyaf, Jemaah Islamiyah and other radical factions have regrouped here. We’re met by Jolo Mayor Alkramer Rasul Izquierdo, who’s somewhat enthusiastic about his town despite Jolo being known as one of the most dangerous placed in South East Asia.

MAYOR ALKRAMER RASUL IZQUIERDO: We’re heading to Barangi Sadamudru where the Jolo Municipal Government in cooperation with the Sulu dental society will be having a free medical and dental check-up for our constituents.

HARLEY: Only in Sulu would a free dental check-up necessitate ten heavily armed police. Any pain inflicted here today is welcome. It’s nothing in comparison to the intimidation and extortion the locals have suffered at the hands of the extremists over the years. Clinics like this are part of a hearts and minds campaign to pull the communities together and shut the terrorists out. While the carrot of community services is being offered, it’s the Philippines military on Sulu who are attempting to take the stick to the terrorists.

The military has more than two thousand troops here but success in trapping the extremists is far from assured.

BRIG. GENERAL NEHEMIAS PAJARITO: [Armed Forces, Philippines] It’s rarely that we can locate them when they are assembled as a group – 20 or 30. Most of the time they are broken down into small teams – 2, 3 or 4 - especially when they undertake kidnappings or other violent activities. And the most difficult one is when they are embedded into the civilian population as they have the support of their immediate families, their friends, their relatives and all the other people in the village.

HARLEY: The military’s current strategy is to deny the terrorists their rural havens.

BRIG. GENERAL NEHEMIAS PAJARITO: We are now here in Particul, one of the municipalities of Sulu, and Particul municipality is the area of operations of the Abu Sayyaf group. For the past month this group has splintered into small groups and we are going after them.

HARLEY: Just out of town, proof of some initial success. Villagers have returned after years of seeking sanctuary in the city – a semblance of normality. Denied their country sanctuaries, the Abu Sayyaf strike at the urban population. In the heart of Jolo a mixed community of Muslims and Christians is targeted.

MAYOR ALKRAMER RASUL IZQUIERDO: There were three killed in this house. One is eight months old.

HARLEY: Four Christians died along with two Muslims. Religious harmony is not part of the Abu Sayyaf’s agenda.

MAYOR ALKRAMER RASUL IZQUIERDO: Here on this corner were lying the mother, the daughter and the husband and two daughters also lying right there.

HARLEY: The massacre occurred just three hundred metres from a military base, yet no soldiers ventured out when the shooting started.

[UNIDENTIFIED PERSON] These are the entrance holes that killed father and seventeen year old daughter who was about to graduate this March.

HARLEY: At the end of our first day in Jolo, old friends catch up. Lito started his career here as a young lieutenant, leading a squad of seventeen men.

COLONEL ANGELITO CASIMIRO: [Introducing man sitting next to him at dinner] And this guy was one of my platoon mates.

HARLEY: Five of them were killed on that first tour. Henry Elumbaring is the only one left. Those who weren’t killed got out. He’s also one of the most experienced counter terrorist officers on Jolo. That makes him a prime target.

HENRY ELUMBARING: In my home town, when you are off duty you can go and work in the rice fields to plant crops, but here if you are off duty, you will just stay in your home – especially with this job.

HARLEY: As the evening progresses, the old hands reminisce, the young Turks listen and learn. But outside in the street, someone else is also listening and waiting. Before the sun rises, one of these intelligence officers will be gunned down.

It’s sixty thirty in the morning here in Jolo City. About fifteen minutes ago five shots rang out in front of the hotel here. I’ve been confined in my room by Colonel Casimiro and his men but what we’ve found out is that Henry, our guest at dinner last night and the last surviving member here in Jolo of Colonel Casimiro’s original squad of seventeen people, has been shot. We’re not sure if he’s alive yet but it doesn’t look good.

Henry is dead but in this lethal game, grief comes a distant second. For Lito information has to be gained, shared and analysed. The war goes on. Henry had risen early, checked the parameters of the hotel then gone to the bakery next door. His assassin shot him point blank in the back of the head, then escaped into the neighbouring slums.

With Lito now trying to track down Henry’s killer, it was left to the local military commander to put the pieces together.

BRIG. GENERAL NEHEMIAS PAJARITO: The most probable suspect here is Iting Sailani. He is an underground terrorist group believed to be connected to JI. He is the local counterpart.

HARLEY: He is an associate, a person you think involved in the killing of Henry Elumbaring, is an associate of JI?

GENERAL PAJARITO: Yes that is what we believe. He is one of the support elements or the local counterpart working for the JI.

HARLEY: Filipino journalists who’d been flown in to report on recent military successes were now filing reports on Henry’s killing. I intended to join them as they prepared to venture out on the streets of Jolo but the Colonel blocked that. Convinced that JI were behind Henry’s death, allowing an Australian out onto the streets was simply beyond the pale.

COLONEL ANGELITO CASIMIRO: No you can’t go. We’re going to talk to the local journalists to take the footage for you because I’m sending you off on the next plane out of this place.

HARLEY: Why is a foreign journalist a liability?

COLONEL ANGELITO CASIMIRO: First you’re white, second your eyes are blue, third you are an Australian and the ASG are working hand in hand with JI and JI hate the Australians so much.

HARLEY: There’s a Muslim cemetery near Zamboanga, Islamic extremists killed by security forces are known to have been carried here and buried before sunset, according to Islamic practise. Henry passed by this island on route to his final resting place. His death was little more than a footnote in the national papers.

For Lito’s team, a good man and close friend had been lost. A cruel reminder that this conflict is far from over.

COLONEL ANGELITO CASIMIRO: For the past eighteen years, we’ve been working hard, trying to make a difference and yet we believe our best is not enough.

HARLEY: Do you think it’s going to change in the near future?

COLONEL ANGELITO CASIMIRO: There is always hope for everyone, not maybe in my lifetime. Maybe in the future.