Nettie comes to live with Celie and Albert not long after Celie and Albert get married. Alphonso, the man the girls know as Pa (though he is not their birth father, as they find out later), is threating to rape Nettie just as he has raped Celie many times before. Celie has already had two children by Alphonso, products of rape, and Alphonso gave the children away to a young couple who could not have their own children.
Even before Celie gets married, she realizes that Alphonso "be looking at Nettie," and she tells Nettie to marry Albert and "try to have one good year" in her life. However, when Albert asks Alphonso for permission to marry Nettie, Alphonso refuses—probably because he wants Nettie for himself—and persuades Albert to marry Celie instead.
When Nettie does arrive to live with Celie and Albert, Celie says that "she [ran] away from home." Nettie felt bad about leaving their new stepmother, but Nettie "had to git out, maybe fine help for the other little ones." They know the boys will be safe because "they can stay out of [Alphonso's] way." Alphonso likely started coming after Nettie, intending to rape her as he did Celie, and so Nettie ran off before that could happen.