The film opens in Lithuania, featuring a young girl beginning to create a portrait. The narrative then transitions to Imperial, Nebraska, where Todd Burpo (Greg Kinnear) is busy installing a garage door for a local warehouse. Todd is not just a handyman; he also serves as the high school wrestling coach, a volunteer firefighter, and the pastor of the local Wesleyan church. Currently, he is on medical leave due to a broken leg sustained during a softball game, compounded by ongoing issues with kidney stones. Despite their financial difficulties, Todd’s wife Sonja (Kelly Reilly) insists on family travel to Denver with their children, Cassie and Colton (Connor Corum), marking Colton's film debut. In Denver, the family visits a butterfly and spider sanctuary where Cassie bravely holds a tarantula while Colton is too frightened to do so.
However, their fun takes a dark turn as both Cassie and Colton fall ill on the return trip. Days later, although Cassie's condition improves, Colton’s fever escalates, prompting a visit to the hospital. There, the doctors reveal that Colton’s appendix has ruptured and requires emergency surgery, cautioning Todd and Sonja to brace themselves for the worst. In the tense moments leading up to the operation, as Sonja reaches out to friends for prayers, Todd seeks solace in the hospital chapel. In an emotional outburst, he questions God about the trials he has faced, stating that while he can handle his own suffering, needing to confront the potential loss of his son is simply beyond him.
Miraculously, after the surgery, Colton pulls through and soon shows a newfound fearlessness, even expressing a desire to hold the spider he previously avoided. Todd and Colton revisit Denver for that purpose, and while at a playground, Todd curiously inquires what prompted Colton's change of heart about the spider. This moment leads to Colton's astonishing revelation — he claims to have visited Heaven and met Jesus. Describing an experience where he left his body during surgery, Colton tells Todd he witnessed both parents in different rooms and ventured into the church, ultimately reaching Heaven, where he heard angels singing. Todd is both amazed and perplexed by these accounts.
As the story unfolds, Colton shares vivid details about Heaven, including the multi-colored horse Jesus will ride upon His return and the wounds that bear testimony to Jesus' crucifixion. Affirming that all will be well, Colton also points out that the images of Jesus they have at home don’t accurately represent him. Once back at church, Todd feels compelled to share his son’s experiences with the congregation, prompting widespread attention and even a feature in the local newspaper. However, not everyone is convinced; some skeptics in town question Colton's story, leading to Cassie defending her brother by confronting bullies at school, an action Todd chooses to overlook.
Struggling to reconcile his son's claims, Todd seeks counsel from friends and a psychologist, the latter suggesting that Colton may simply be experiencing a hallucination triggered by the trauma of near-death. Similarly, Sonja grapples with disbelief, suspecting Colton might be weaving together various stories he has encountered. Tensions rise during a church board meeting led by organist Nancy (Margo Martindale) and Todd's best friend Jim (Thomas Haden Church), who express concerns over the divisiveness Colton’s story may incite within the congregation, potentially threatening Todd’s pastoral position.
After attending a funeral for a man who perished in a fire, Colton shares a touching account of meeting Todd's grandfather, Pop. Todd shows Colton an old picture of Pop as an elderly man, but Colton insists that no one in Heaven is old or wears glasses. Upon discovering a younger picture of Pop, Colton asserts that's the person he encountered, providing Todd with a spark of belief that perhaps his son genuinely visited Heaven. The plot thickens when Colton reveals to Sonja that he met his sister she lost to miscarriage years prior, describing her appearance in a way that unnerves the couple, as they had never disclosed such details to him.
As Colton's story garners national attention, Todd is unexpectedly contacted by a radio station, thrusting him into the spotlight on-air to confirm Colton's claims. Undeterred, Todd invites the community to their church service that Sunday, leading to emotional congregation members as he recounts their family's ordeal since the surgery. The audience is moved when Todd declares his heartfelt belief in Colton’s Heaven visit. Sonja joins him, followed closely by their children, fostering an outpouring of warmth within the congregation.
In reflective closing moments, the Burpo family is seen at home, with Todd watching a news report featuring the Lithuanian girl from the beginning, who has painted a unique portrait of Jesus that deeply resonates with Colton, revealing he recognized the likeness of the Jesus he encountered in Heaven. The film concludes with updates about Todd's continued pastoral role, the family's addition of another son, and Colton as a teenager, while Cassie humorously remarks that he is no angel.
