Their only refuge is Kenya...if they survive.

Among the boys are NOAH and SIMON MIAK-- fraternal twins. And although they are suffering they do not lose their faith in Jesus, even though their brother Matthew was taken from their village by Muslim invaders and those around them chide them for their strong belief. Among those who are not believers is KAI, who during this horrendous journey reads from the journal Noah keeps religiously, and there begins the history of brutality and sacrifice.

In 1978 Noah and Simon are born in a small birthing hut in Southern Sudan, while his great Uncle, clutching a Bible, keeps watch for Arab invaders on the outskirts of the village. Inside another hut Simon’s and Noah's father, ISACC, awaits their birth. Deeply religious, he prays while his brother KUMI, a hater of Christianity, watches with disgust. And so the brothers are born into a family rife with religious disparity, while they must also face life without their mother who died in childbirth.

Five years later Isaac remarries -- a Christian wedding officiated by PASTOR NORTH who will become a mentor to both Noah and Simon. On the day of the wedding Isaac’s older brother Minkah, who calls himself Mohamed, returns home with his daughter Azemera. That evening Minka warns his family that the government has declared Sharia law for all of Sudan and that there will be no more Dinkaland if the law is enforced-- they must convert to save themselves; something the others do not want to do.

As they talk soldiers enter the village. Among them is KOBI, cousin of Issac and Kumi. Issac is drawn into the past remembering how things came to be this way many years before when his given name was Johari. Pastor North persuades Johari’s father, Chief Lutalo, to send Johari and Kumi to his Christian missionary school, despite the protests of their mother who insists they are needed to look after the cattle. But their father insists knowing that the education they will gain will someday greatly benefit the boys and the village. He also insists that his nephew Kobi join his sons.

Months later Minkah and Kobi run away from the missionary school, leaving Johari and Kumi behind. Pastor North tries to calm Johari, whose Christian name is now Isaac, and persuades him that staying at the school is the best thing. But Isaac is not convinced, nor is his brother Kumi who pretends to be asleep while he listens covertly. Tucked beneath the sheets of his bed is a knapsack, and Kumi is fully dressed to make his escape. When Isaac and Pastor North leave the room, Kumi makes his break past the other sleeping boys.

Years later, and ready to graduate, Isaac learns that his cousin Kobi has left the village to join the resistance and his brother Minkah has converted to Islam. Isaac has been ordered home to take a bride. It is then Pastor North tells him, "Don't let pagan rituals or man's traditions destroy the work that the Lord has done in you."

When Isaac returns home his faith clashes with the traditions of his family and he refuses a planned marriage. When he does marry the woman of his choice, they have three sons: Matthew, Noah and Simon, who also attend Pastor North’s school. It is Pastor North who gives Noah the journal that will one day chronicle his life.

When the school is burned by the villagers to keep the rebels from destroying it, Noah’s faith is sorely tested but remains strong. Noah and Matthew sit watching villagers get baptized in the Nile River, as Noah writes in his journal that it is his day of baptism also. But it is not to be as helicopters suddenly swoop in from the north and attack their village.

Gunners in the helicopters shoot into huts, as Arabs on horseback round up the villagers. Terrified villagers scatter and others are killed by the hail of bullets. Noah and Simon make their escape with other Dinka boys, but Matthew is captured and enslaved by the invaders. During their long trek Noah and Simon are joined by other "Lost Boys" escaping physical and spiritual enslavement, as Matthew lies in a hut owned by his captures. He prays to his God, "Dear heavenly father, I plead the blood of Jesus over my life. Protect me, help me, please." When Matthew makes friends with another captured Dinka boy, he is told, "Black slaves, especially Christians, are viewed lower than animals." It is during his enslavement that Matthew eventually falls in love with another slave named Elizabeth, who like Matthew hides her faith.

Rebel forces find the "Lost Boys" during their long trek.

Among the SPLA rebel soldiers is Simon's and Noah’s cousin Kobi, who tells them he is taking them to Ethiopia where they will be safe. The boys don’t want to go -- they want to go home, but Kobi tells them there is no village to go home to. He asks Simon and Noah to join the rebel soldiers but they refuse. At the SPLA camp they find Pastor North, who finds the treatment of the lost boys in the camp intolerable. And here Simon and Noah become divided; Simon believes the SPLA is now his family and wants to help the Dinka Boys, while Noah simply wants to go home. Kobi believes that Noah is a traitor and tells Simon to kill Noah. Pastor North meets Noah one night to help him escape, but Simon finds them. Pastor North steps in-between Noah and Simon’s bullet and is severely wounded. Noah makes his escape and eventually makes it to the refugee camp.

Matthew and Elizabeth escape their years of bondage and flee, only to have Elizabeth drown in the Nile river. Matthew also makes it to the Kakuma refuge camp.

Years later Noah, Matthew, and Simon have immigrated separately to the United States, unaware that someday they will be brought together again at the National Lost Boys and Girls conference in Boston. And it is at this conference Matthew discovers Elizabeth -- lost to the Nile all those years ago -- has survived and is living in the states.

At last the "Lost Boys" are truly home and lost no longer.