An East Timorese journey

CNN's Maria Ressa

(CNN) -- Jakarta Bureau Chief Maria Ressa has witnessed East Timor's transition from Indonesian-occupation to independent nationhood. As East Timor prepares to go it alone, she revisited some of the people and places that have for her defined the new nation's traumas and hopes.

As East Timor celebrates its independence there's an air of celebration -- but underneath, much fear, sorrow and loss.

Traveling for 18 hours in one day, I revisited the places and remembered some of the people I met when I was first assigned to Indonesia in 1995.

There was the young governor's assistant Basilio Diaz de Arraulo, who years later became the political voice for militia violence.

Now he lives in Jakarta.

There's the guerilla leader of Falintil, the resistance fighters who fought a bitter struggle against Indonesian forces for more than two decades.

Remains of the day: East Timor has had first hand knowledge of many atrocities

Their leader, Taur Matan Ruak, made the tough choice of holding his men back in their jungle camps as the militias wrought their deadly revenge on the people of East Timor in 1999.

His decision left his people defenseless and led to the destruction of much of East Timor, but helped his nation avoid a civil war and paved the way for outside intervention by a force of international peacekeepers.

Today General Taur Matan Ruak heads East Timor's new army, the East Timor Defense Force.

Interview with imprisoned Gusmao

Then there is Xanana Gusmao -- the poet fighter turned founding president of independent East Timor.

I first interviewed him in Jakarta's top security Cipinang prison, where he was jailed for subversion following his capture by Indonesian forces in the early 1990s.

Through the years I saw how he became the inspirational voice for his people. Now he is the president of his nation.

I began my journey through East Timor in Suai, about six hours drive from the capital, Dili.

In 1999 the first signs of the terrible violence to come was in the church in this remote mountain town.

As early as January, 6,000 pro-independence supporters had flocked here for refuge against militia attacks -- many of them staying until the August 30 vote.

Among them was Faresh da Costa who worked for the parish priest Father Hilario Madera.

The priest was a key figure in the town, negotiating for the refugee's safety with the militias and the Indonesian military.

Shortly before the independence vote on August 30 that year, the men in the church compound began to prepare for war. But they never got the chance to fight.

After an overwhelming majority of East Timorese voted for independence, Father Hilario asked the men to flee to the mountains, leaving only the women and children.

Days later on September 6 the militia attacked -- Faresh was one of only nine survivors.

"They attacked at two in the afternoon," he recalls. "We couldn't escape because the military and the police surrounded us while the militia attacked from the front gate."

He said Father Hilario came from the back of the compound, telling people to go back inside while he tried to reason with the militia.

"I was so scared I couldn't feel my hands," he told me. "People were shooting guns and throwing grenades."

The militia in Suai and across East Timor were heavily armed -- their weapons given to them by the Indonesian armed forces.

Faresh survived because he hid -- Father Hilario was killed.

Today, there is a small cross marking his death. The keys to the church and his watchband kept in a small coffin.

Outside there is a much larger memorial -- dozens of gravestones, each name bearing silent witness to a violent death.

The church itself, once a refuge, remains unfinished -- now a mute testimony to the violence that failed to the kill the dreams of a people.

Indonesian's pledged money

But life goes on.

In a small village about an hour and a half away from Suai Nemecio Lopes de Carvalho, one of the main commanders of the militia group that attacked the church has returned home.

In what's left of his house, I remember interviewing his brother Cancio, a key militia leader who accused the UN of rigging the vote for independence.

Nemecio says he still believes the vote was unfair, but admits that his side also violated the rules of the game.

"The Indonesian government pledged money to us, gave guns to us," he says. "So it was fraud, it was irregularity."

After so much violence, there is a cry for justice beneath the surface of life here.

Restricted to his town, Nemecio says he's willing to face the courts.

He says he has told his men to return from Indonesian West Timor where they fled after the arrival of the peacekeepers.

"Face it, don't run away from it," Nemecio says. "Let's come home, let's go to jail together, let's die together."

He says it is time to move forward for the sake of the next generation of East Timorese.

On the question of justice and reconciliation he says it's not just the militias who should pay.

Speaking to me he named seven Indonesian generals, including then Armed Forces Chief, General Wiranto, who Necio said exhorted militia leaders to destroy East Timor if the vote goes against them.

Wiranto himself has repeatedly denied any involvement in the violence in East Timor.

That's nothing short of a lie says Nemecio – adding that he is willing to testify before an international tribunal.

"Indonesian diplomats, the Indonesian government, politicians came to us and promised – just continue struggling for integration. 'We have arranged it with the U.N.' they said. It was just a formality.

"I was used, fooled, tricked by the Indonesian government."

Another three hours away, back up in the mountains we arrived in the village of Memo.

In 1999, two days before the vote, the militia attacked here.

Our team in East Timor got to Memo within minutes of the attack and found what they had left -- homes burned to the ground, lives shattered, unknown numbers killed.

Joaquim Lopez came home to find his house destroyed , his wife and child missing, his uncle and brother murdered.

When the police came he accused them of helping the militia.

Today he has rebuilt his home. Despite his initial fears his wife and child survived and are by his side.

He says he's lucky compared to his neighbor, Engracia Casmira.

In 1999 our team found her weeping inconsolably, walking down the village's main dirt road appealing for help after the militia killed her husband.

Nearly three years later, she tells me how difficult her life has been. Her daughter is sick and she has no money to buy medicine.

"No one's helping me, the government doesn't care," she says. "I'm so alone. I don't even have enough money to buy clothes. My child doesn't have anything."

She told me repeatedly her husband died for Xanana.

In many homes in this small village the walls carry pictures of East Timor's new president.

For many he is a sign of hope to get through these difficult times.

Memo's story is repeated again and again across this emerging nation, and East Timor's people will continue to bear the scars of their struggle for many years to come.

"We sacrificed our lives," says Joquim Lopez, "but it was worth it."

His brother's grave is near his house. Inscribed on it a simple motto in Tetum, East Timor's native language.

It reads "Mate maibe sei manan fun" -- "I died but I won the war."

For the survivors of East Timor's fight for independence, this is a time to rebuild -- their homes, their lives and their nation.

For me this journey through East Timor's struggle has been long and exhausting, but from the people I've met I see hope that tomorrow will bring better days ahead.