Children of Eden begins at the beginning. The show opens with God seeking to "Let There Be" a universe complete with plants and animals. Not satisfied, he creates Adam and Eve, and tells them they have only to be good and grateful children. Adam assures Father (God) that he will be "Good".

Adam and Eve eventually eat from  the Tree of Knowledge and are tossed out of the garden. They continue life in "The Wasteland" where their sons Cain and Abel are born.

Their lives become good but Cain craves more. An amazing but frightening discovery leads to a "Clash of the Generations". Abel loses his life in the struggle. The murderous Cain is struck down by God with a mark his descendents will wear for generations to come.

Years, later, Eve recants to Father how Adam never stopped looking for Cain, but how life has moved on with their new son Seth. Eve then joins Father in heaven leaving the earth to the "Children of Eden".

Act II of "Children of Eden" opens with a tour of the "Generations" from Adam through Noah. Following the tour, Noah speaks to God about reconsidering his decision to flood the earth. When God refuses, Noah continues the preparations, including seeking the right wife for his son Japeth.

Japeth, though knowing his wife should be of the race of Seth, falls in love with Yonah, the family servant girl who wears the mark of Cain. All chaos breaks out shortly after he announces his decision to the family.

Fearing the flood, Japheth persuades Yonah to stow away on the Ark. After "Forty Days and Forty Nights" come and go, the family discovers her. Noah, going against a clear order from God, allows Yonah to remain and marries her and Japeth.

Shortly after the wedding, the rain ends and a dove appears with an olive branch. Mama Noah sings of how good it is to see the sun again. The family disembarks and sets about to rebuild the world with the next generation of the "Children of Eden".