"Children of the Storm" begins as the narrator, Natasha, describes a family trip to visit her father, a pastor who has been imprisoned in a Siberian camp by the Soviet state for spreading the message of Christianity. The narrator explains how, for years, her family has been persecuted by the Soviet state, which has mandated atheism as the national religion. Christians are forbidden from attending church. Anti-Christian sentiment plagues Natasha everywhere she goes, including at school, where she is pressured by teachers to declare allegiance to the Soviet state. She is humiliated by her classmates and her teachers, who deride her for worshiping Christ.
As Natasha grows older, she witnesses many a Christian lose opportunities as a result of his faith. They are denied employment and admission to college. She begins to wonder if she is willing to sacrifice her future for the sake of her faith. She is further tempted by friendly atheist teachers, who pressure her to question her beliefs. Shelya Abromovna, for instance, argues that the Bible is outdated and scientifically inaccurate. Shelya also persuades Natasha that her future is bleak unless she turns away from religion, as she will be denied higher education and a creative profession.
While in high school, which is called university, Natasha seriously doubts Christ and questions the Christian faith. But she reflects on the witness of her father, who has endured persecution and imprisonment for the sake of his faith. During her last year of high school, Natasha repents for having rejected Christ and formally accepts Christ at a youth group meeting. Natasha's grandmother is imprisoned for worshiping Christ, and Natasha wants to visit her to comfort and pray with her. When her nursing school refuses to let her visit her grandmother in prison, Natasha finds a nurse who excuses her from class for health reasons. She is immediately expelled from school, and she is devastated.
Natasha prays for inspiration and strength from the Lord to endure persecution and tribulation. She feels called to promote the word of God by printing and distributing Bibles and Christian literature. Her father, who has been released from prison but is now in hiding, helps her by putting her in contact with other Christian leaders. He blesses her to travel all over Russia delivering suitcases of Christian books to pastors. During this time, the Lord protects Natasha from harm. At the end of the book, Natasha's family is reunited, as the Soviet regime is losing power. Her family praises God for protecting them (many Christians lost their lives) and for the many blessings He has bestowed upon them.