Further years of oppression followed as the Indonesian military tried and failed to wipe out resistance.
Barely a family in East Timor was not touched in some way by the Indonesian invasion in 1975.
Within four years a third of the population had perished from bombing, starvation and systematic killing.
Further years of oppression followed as the Indonesian military tried and failed to wipe out resistance.
Throughout the Indonesian occupation the Catholic Church was the first line of defence against human rights abuses. Nuns and priests acted as counsellors, comforters, and protectors of the people - there was no where else to turn.
Now, as East Timor heads towards an independent future, the serious problem of long term trauma in society is starting to be addressed.
Jose Antonio Belo - arrested seven times - belonged to the underground movement known as Calendestine. He spent many months in the notorious interrogation centres of the Indonesian special forces.
"Sometimes we detainees were not let out from the room for a few weeks.
"They'd just give us food two or three times a week - and they didn't let us go to the bathroom - they just provide us small basket - we had to sleep there, and eat there like a dog."
Drugs and alcohol
To meet the serious after-effects of such trauma a new Australian-funded psychosocial support group, Pradet, is attempting to set up the beginnings of a mental health service for the territory.
Its director, Christina Tang, says long-term trauma is manifesting itself across East Timoese society.
"For young people it's often anger and aggression particularly with no schooling, no education, unemployment, high levels of uncertainty and no future," she says.
"What were seeing at the moment are young people just roaming the streets - some are turning to alcohol and drugs.
Unwanted children
"Someone who has psychosis for example, and is then traumatised, will be at higher risk and unfortunately what we're seeing is people being tied in their homes or beaten in public or abused or being put into prison."
But the scale of domestic violence, hidden by the war, is only now being acknowledged.
One woman told a story typical of many.
"He used to beat me and the children, especially when he was drunk," she told me. "I would go to the church and ask for advice.
"Maybe this is God's test for me I thought, and I prayed and I tried to be calm and be patient."
Tired of the beatings and her husband's womanising, eventually the woman left him and sued for divorce.
Bitter legacy
Violence has now become ingrained in society and though the Indonesians have gone, they have left behind them a bitter legacy of destruction and division.
Those who suffered are being asked to forgive those who collaborated with the enemy - culminating in the militia members who caused such murderous havoc just one year ago.
It is a message endorsed by Timorese leaders in the cause of reconciliation. But Dili priest Father Jovito says people need more time.
"People are very traumatised," he says. "They lost everything - especially those who faced the violence directly.
"It's very hard to accept talk of reconciliation. People still face the reality that everything remains the same - destroyed - it's a nonsense that people should accept criminals amongst them.
We should talk and try to reconcile people but not now."