Alphonso, the man Celie thinks is her "Pa" or father, although he is actually her stepfather, is the father of her children. Alphonso had the role of a father to Celie and was supposed to protect her. Instead, he rapes and impregnates her, then farms out their two children to be raised by another couple.
This is a disturbing beginning to the novel, but Walker has stated that she wanted to portray the experience of rape from the female point of view, which she says was seldom done at the time she wrote the novel. These experiences of rape, impregnation, and losing her children are traumatic and scarring for Celie, especially because Celie has no way to escape from assault in her own home.
However, Celie uses what little control over her life she has to protect her younger sister, Nettie, a highly intelligent girl. Celie, for example, enters into a marriage she does not want with Mr.__, who is looking for a mother for his children, to protect Nettie from that fate. Due in large part to Celie's help, Nettie is able to avoid an early marriage and obtain an education. Celie herself is eventually able to escape oppression and reunite with her children.