Set in Burleson, Texas, between 2008 and 2012, the film centers on a 10-year-old girl named Annabel Beam, daughter of Christy Beam. One day, Anna starts to vomit, and when examined by her doctor, he does not find anything abnormal. On March 20, 2008, Anna wakes up her family at midnight because of an intense stomach pain, severe enough that her parents decide to take her to the hospital. Doctors find no signs of illness, except to say it could be either acid reflux, or lactose intolerance, but Christy is not convinced by this.

The following morning, Christy finally finds a pediatrician in the hospital that is able to diagnose Anna with an abdominal obstruction, and he tells them he must operate immediately or she will die. After the emergency surgery is performed, the doctor explains that Anna has been left with pseudo-obstruction motility disorder and she is unable to eat, so feeding tubes are needed for her nutrition. The doctor then tells the Beams about America's foremost pediatric gastroenterologist, Dr. Nurko, who practices in Boston, but explains it could take months for them to be seen. In January 2009, Christy and Anna travel to Boston despite not having an appointment with the doctor.

Dr. Nurko has a last minute opening, and when Anna is subsequently examined at Boston Children's Hospital, the extent of her chronic illness is found. She then goes through extensive treatment. During this ordeal, Anna and her mother befriend a local Massachusetts resident named Angela, as well as Ben and his sick daughter, Haley.

On December 29, 2011, Anna, along with her bigger sister Abbie, climb up to a very high branch of an old cotton tree. While they are on that branch, it begins to break. Anna goes to the trunk for safety, whereupon stepping on it, she falls in a hole to the base of the tree. When Christy finds out what has happened, she desperately calls her husband, as well as the fire department. Anna is then rescued by the firefighters, who warn Christy to expect the worst by saying that nobody could fall 30 feet without sustaining a serious injury; broken bones or paralysis. Once out, Anna is airlifted to a hospital, where a battery of tests are run on her, and all of the tests come back negative. Other than a minor concussion, Anna is uninjured.

Sometime after the fall, Anna seems to no longer be affected by her illness. When Christy and Anna go to an appointment with Dr. Nurko, he tells Christy that Anna is miraculously cured. Anna then recounts with her parents the experience she had during the fall. She describes how her soul left her body during the fall, and God promised that she would be cured of her illness upon her return to Earth. At church, Christy shares the story of how God miraculously healed her daughter with His love. As Christy finishes her speech, one of the congregation protests, stating that he does not believe Christy. Ben, who has traveled from Boston upon hearing the story about Anna, believes her and tells her that his daughter Haley died peacefully because Anna gave her faith when in the hospital.