We are dying as a people and as a nation.

Carlos Belo, Bishop of Dili, 1989 

ABRI also suffered heavy casualties at the hands of FALINTIL (FRETILIN's army). Australian intelligence analysts estimated that there were more than 450 Indonesian military casualties in the first few weeks, and in the first four months of 1976, as many as 2000 Indonesian troops were killed. 

This was largely because FRETILIN had expected the invasion for months. Well before December 1975, it had begun to establish bases and relocate its forces in the country's interior. With 2500 former full-time Portuguese troops, 7000 part-time militia, 10,000 reservists—plus civilians who had received military training following the civil war with the UDT—FALINTIL had a formidable contingent of fighters. In addition, it had a detailed knowledge of East Timor's geography and large supplies of weapons left by the Portuguese. 

As a result, FRETILIN was able to maintain effective control over the majority of East Timorese territory for many months. Within the liberated areas, life continued as usual—schools and agricultural cooperatives continued to function, and FRETILIN radio continued to broadcast throughout the territory. 

But beginning in September 1977, things took a turn for the worse. ABRI's plan was to push the resistance into the center of the country, where the fighters could be killed or captured, and to force the rural population to the coastal lowlands, where they could be more easily controlled. (Catholic sources called this "encirclement and annihilation.") 

Using tens of thousands of ground troops and counterinsurgency aircraft called Broncos (newly acquired from the US, they were ideally suited for the rugged terrain of East Timor), ABRI forces began penetrating the interior of the island. Along the way, they bombed forested areas to defoliate ground cover and used chemical sprays to destroy crops and livestock. 

Lourenco, a former UDT supporter who later began working with FRETILIN, described the annihilation of a section of FALINTIL's eastern zone: 

I was in Matebian [near Baguia], where it's all mountain and rocks....On 17 October 1978 some Indonesians got right to the bottom of Matebian mountain and that's when we started to fight back. For those first two months, October and November, we were very successful and about 3000 Indonesians died. Then they got angry and scared to come close and started to bomb us from the air. 

They bombed twice a day, in the morning and afternoon with four black planes. Their name I know now is Broncos, but we called them scorpions because they had a tail that curves up at the back like that insect. Their bombs left a big hole about two meters deep. 

Then they got new supersonic planes. Our people were very frightened of those because you didn't even hear they were there until they were gone. Those supersonics would zoom along the valley so fast we couldn't shoot them.... 

We knew by radio from the south zone that the Indonesians had dropped four napalm bombs there. Then they dropped two of these on us. I saw all the flames and heard people shouting and screaming. I was on another mountain but I could see well....By foot it took half an hour to go down and up again, and by the time we got there everything was completely burnt. 

We saw a whole area about fifty meters square all burnt, no grass, nothing except ash. On the rocks it was a brown reddish color and on the ground ash too, not ordinary grey ash, a sort of yellow ash, like beach sand. You couldn't see where bodies had been. There was nothing except ash and burnt rocks on the whole area, but we had heard those people screaming.

In 1979 all our people, nearly 3000 from my Laclo area, were caught by the Indonesians near the main coast road where you pass to Manatutu and Baucau. We go to the highest point and stayed there for a month trying every way to get out. 

The Indonesians attacked us from the beach and from Manatutu, Dili and Baucau. All came together and surrounded us. Some fighters escaped and took guns back to other FALINTIL. I was captured because I was responsible, that was my position, I had to stay with my people, I couldn't leave. They captured me without my gun or I would be dead. 

We were interrogated, but we spoke no Bahasa Indonesia so a Timorese interpreted. He said, “Don't be afraid, always say something, say anything.” The interpreter made up our answers. He was Timorese too, he tried to protect us. There were so many people to interrogate and we were all telling wrong things anyway. But when they took us to Dili, slowly they wiped out nearly all of us who'd been fighters. Spies and informers had time to do their work there.

Its forces and weaponry devastated, FALINTIL was nonetheless able to regroup and reorganize—a pattern that was to be repeated several times in the next decade. Under the leadership of Xanana Gusmao, a local commander in the east, FALINTIL reorganized its forces into small, relatively independent units throughout the country. 

The change in strategy and organization allowed it to mount more attacks on ABRI in 1980 than during the eighteen-month encirclement and annihilation campaign. Although FALINTIL couldn't reestablish control over any population centers, it was able to build a covert support network within Indonesian-controlled villages and to regain control of significant amounts of rural territory. ABRI casualties mounted and morale declined. 

By March 1981 FRETILIN had established enough communication among its units to hold a national conference. There Xanana was elected head of FRETILIN and commander-in-chief. 

In response to FRETILIN's resurgence, ABRI launched a new operation in mid-1981 that included something called a "fence of legs." About 80,000 East Timorese males, ranging in age from 8 to 50, were forced to walk in a line across the countryside in front of ABRI troops, protecting them from attack by FALINTIL guerrillas. The objective was to either flush out the guerrillas or to force them into the center of the island where they could be massacred. A participant, Cristiano da Costa, describes what it was like in one of many areas after the campaign: 

It started from all parts of East Timor, all driving towards Aitana, near Lakluta, that was to be the middle of the circle. The front line was Timorese forced to take part. When the circle was small enough, the army bombarded the area, then soldiers went to finish off any people left there. 

One week later I was forced to go up with a group of soldiers to do a final clean-up....We smelt the bodies before we found them. The heads had been cut off the first bodies, one woman and four men....The heads were on the other bodies I saw. We found three other men tied by the feet hanging upside down in trees...another two men were tied with their hands behind the trunks of trees. Their faces looked beaten and it looked like knife wounds to their stomachs. 

On the ground beside them there were six others, two women and two children and an old man and an old woman....There was dried blood on those bodies....The smell was very bad and the flies....It was not possible to identify those people; if they were my own brother or sister I could not know them.

While many FRETILIN groups surrendered or were slaughtered during the campaign, many evaded capture. By late 1982, FRETILIN had again reorganized and was launching a number of attacks all over the country (including one on Dili), putting local Indonesian military leaders increasingly on the defensive. A number of the officials decided to negotiate cease-fire agreements with FRETILIN, culminating in a country-wide cease-fire agreement on March 23, 1983. (ABRI and the Indonesian government hoped to keep the cease-fire secret and were greatly embarrassed when the news broke internationally.) 

Within five months, however, ABRI Commander-in-Chief Benny Murdani unilaterally broke the cease-fire, declaring, "This time no fooling around. We are going to hit them without mercy." On August 17, 1983, Indonesia launched a new campaign. 

But since FRETILIN had taken advantage of the cease-fire to consolidate its underground network in the resettlement villages, it could resist fiercely—even though it faced massive numbers of ABRI troops, as well as bombing from the air and sea. Once again, ABRI wasn't able to make any significant gains, and withdrew its troops to the major roads and population centers at the end of 1984. 

During the latter half of the 1980s, ABRI launched a number of offensives, hoping to capture Xanana Gusmao, and it continued to use "fence of legs" operations. But, in large part, the military situation remains stalemated. ABRI's 15,000–20,000 troops control the main towns and other strategic locations, while FALINTIL's 1000–2000 guerrilla fighters roam the countryside. The resistance continues to have an extensive underground network in the towns as well. 

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