The book follows Dellarobia Turnbow, a woman born and raised in Tennessee. At 28 years old, Dellarobia feels trapped in her boring, unfulfilling marriage, as well as her familial duties. One day, she decides to have an affair with a young telephone repairman. However, when she is hiking to meet the repairman, she sees an huge orange blur in the sky (unknown to her, a huge migration of monarch butterflies) which causes her to turn back, thinking it is God's sign of disapproval.
Dellarobia's father-in-law, Bear, wants to clear the mountain of trees where Dellarobia saw the phenomenon for monetary purposes, but she urges them to wait before doing so and investigate first. When she and her family hike up, they discover a stunning sight: a million monarch butterflies covering the trees and scenery. The next day, Dellarobia's husband, Cub, testifies to the Church about the sight, and the community decides how to deal with it. People have mixed feelings, for many believe it is a vision from God, but Bear is still determined to destroy the area.
Dellarobia is visited by news reporters and media stations, but also a scientist named Ovid Byron, who is a long-term studier of the monarch butterflies, and sees their sudden migration as an ominous sign that signifies their pattern being disturbed by global climate change. Ovid warns Dellarobia that the butterflies might not last long in this new environment, and would likely not survive the harsh Tennessee winter ahead. The two become increasingly close as they work together collecting and analyzing data of the butterflies, and they become attracted to each other. Ovid begins to change Dellarobia's long-rooted ideals of that this phenomenon and environmental changes are of God's divine workings, making her see the reality of climate change through scientific lens.
When Ovid's wife Juliet comes to visit, Dellarobia realizes that her dream of having a relationship with Ovid is simply not realistic. However, she also sees that Cub is holding her down, and divorces him.
The butterflies are decimated by a sudden snowfall, but as the weather becomes warmer, Dellarobia and Ovid become hopeful as they see that many of the monarchs have survived. Dellarobia plans to go back to college, and move off the farm along with her children. Just like the butterflies survived, she did as well.