It turns out that Samuel also assumed the children were Nettie's biologically—this is why he was so eager to have Nettie join the family on their mission to Africa. Nettie says they are not her biological children, and asks Samuel to explain where the children were found.
Of course, the children do have a biological relationship to Nettie; Nettie is their biological aunt. It seems that Samuel, too, picked up on the resemblance between the two children, especially Olivia, and Nettie.
Samuel explains that, back in Georgia, many years ago, a black man owned a dry goods store with his two brothers. This store began attracting too many customers for the liking of the white store owners in the town, so these white owners lynched (killed) the three black men and burned down the store. The owner they killed was Celie's and Nettie's biological father.
At last, the story of how the children came to Samuel is revealed, and in the process Nettie and Celie learn of their own true past: that Pa was not their father. Of course, there is the tragedy of racism in the story as well, given that the man was killed by whites who disliked his growing economic power.
Upon learning of her husband's death, Celie's and Nettie's mother then began a long slide into mental illness. A new man began courting Celie's mother—the man Celie and Nettie called "Pa"—and married their mother, despite her mental illness. Pa had many more children by her, and, as the reader knows, goes on to rape Celie and have two children by her as well.
Here is the story of how Pa came into Celie and Nettie's lives. It once again captures what seems to be a trend among relations between black men and women, in which the man is charming and kind in his courtship but, once married, becomes cruel, interested only in control, and sexually abusive.
Pa knew Samuel from the community, and pretended that the children Olivia and Adam were children he had by Celie's and Nettie's mother's, and not by Celie. Pa lied to Samuel, saying that the family was now too large, and that he (Pa) could not care for all his children. Samuel therefore offered to take in Adam and Olivia. Samuel told Corrine, simply, that the children were God's gift to them. Samuel never explained to Corrine the circumstances of the children's origin. Nettie ends the letter exclaiming, once again, that "Pa" is not their biological father.
Nettie is able to piece together this accurate story of what happened from her own knowledge of the story and from Samuel's piece of the story. Nettie, in effect, is writing her and Celie's own true story. Nettie's exclamation that Pa is not their biological father has deep significance. In a novel that displays cycles of violence or bad behavior within families and focuses on resemblance (physical and behavioral) from one generation to the next, it is a tremendous deal that Nettie and Celie are not actually related to Pa, but rather to a loving, successful businessman. It provides them with a different foundation, a different model to replicate, one of love and success and self-possession.