Seven years into a devastating drought in California, Katashi Aki accidentally backs his sanitation truck over a little boy named Ezekiel Junior. The boy’s dying words about going to heaven to be with Jesus change the witnesses on the scene forever.
Four years later, California is ravaged by a series of severe earthquakes and wildfires. The state is declared a disaster area, too damaged to rebuild or inhabit. One percent of the population chooses to remain. Sixteen of these are Christians who have banded together to aid and share God’s Word with those who are too poor to flee. The Holdouts include Ezekiel Junior’s parents, Zeke and Alexis, his sister Sasha, Katashi, and others. They live in a secret underground compound in what was once Torrence, California. Since water is scarce, the Holdouts must always be armed and on the lookout for Mongers who would steal what little they have.
Zeke is startled when, at one of their church meetings, he feels phantom touches and hears voices telling him to listen. At first, he wonders if he’s going crazy. When Zeke feels confident he’s really hearing God, he shares this information with Alexis, their 13-year-old daughter, Sasha, and the elderly Pastor Bob.
Pastor Bob’s beloved wife, Jennie, is suffering from terminal cancer. Bob has announced his plan to leave the mission in California so they can spend Jennie’s final days with family. While Zeke is one of the leaders of the group, Dr. “Doc” Adam Xavier makes it clear he intends to take Pastor Bob’s place as the main authority. Doc is a believer, but he often demonstrates self-centered and arrogant behavior.
The Holdouts deflect several Mongers’ attempts to locate their high-tech compound. Zeke and Pastor Bob visit a tribe of Native Americans with whom they’ve traded, since Bob wants to say goodbye. Bob and Zeke meet a 101-year-old matriarch of the Nuwuwu tribe, named Gaho, and talk to her about the Bible. Gaho’s son, Kaga, is the tribal leader. Although Gaho, Kaga and some members of the tribe believe in God, they still feel they must perform acts and rituals to please Him. God speaks to Zeke, and Zeke tells them about Jesus’ free gift of salvation. The younger members of the Native American family still scoff, but Gaho ponders Zeke’s words.
When someone discovers a manual in Arabic stashed among other books in the compound, Zeke and Pastor Bob grow concerned that an enemy may be in their midst. They notice irregular behavior from a Holdout member named Mahir. They check the infirmary where a young woman named Cristelle is recovering, and they notice her oxygen has been shut off. Mahir is nearby when this happens. Zeke and Doc take Mahir’s guns and lock him up.
Doc tells Pastor Bob that Jennie’s condition is worsening quickly. He doesn’t believe it is wise for Bob to take her away from the compound. Meanwhile, the men select Katashi as an elder. The group will vote in a new leader to replace Pastor Bob. Doc continues to make it clear he believes the new leader should be him.
On their return from a supply run to Arizona, members of the group are pursued by federal agents. Zeke speaks with the agents and learns they are concerned about his dealings with the Native American tribe. He suspects one of the younger tribe members has tried to get the Holdouts in trouble with the government. Zeke rides away from the agents on his motorcycle with the lights off so as not to lead them to the compound. He gets turned around and then hits a bump, damaging the bike.
A Monger named Willard, with whom the Holdouts have butted heads in the past, gives him a ride to the Nuwuwu land. Zeke feels God leading him to pray for and speak frankly with the Monger. Zeke learns Gaho has died and offers prayers and words of sympathy to Kaga. Kaga reveals that Gaho died holding the verse John 3:16, which she’d written out in her native language. He asks Zeke to read it at the funeral ceremony. Zeke feels he must first return to let his family and friends know he’s all right, but he’s excited about the prospect of sharing God’s Word with the tribe.
When Zeke returns to the compound, he learns Kaga’s daughter-in-law, Kineks, has been talking to the feds. Doc ordered medicines, including embalming fluid, from Arizona in preparation for Jennie’s death. The feds know about the medicines and are convinced the Holdouts have something to do with Gaho’s death.
Besides the imminent threat of having their compound discovered, Zeke also has to deal with the vote for the new leader. Doc refuses to postpone it. Mahir is allowed freedom to confront the still-recovering Cristelle, whom he accuses of bringing the Arabic material into the compound. He believes her to be a traitor. With Willard’s help, he attempts to kill her, but doesn’t succeed.
Cristelle provides a logical explanation for the document, which was a letter from her family. Jennie can read enough of the language to confirm Cristelle is telling the truth. Mahir is devastated by the mistake he’s made in distrusting his Christian sister. Cristelle forgives him, and her husband says he will try to forgive as well.
Jennie shares some parting words, and the vote ensues. Doc is devastated when he loses, particularly because it reveals that his own wife voted against him. After a discussion with Pastor Bob, the contrite, humbled Doc returns to apologize to the group. Mahir also begs for forgiveness.
Zeke, the new leader, is still determined to make it to Gaho’s funeral. He invites Willard into the compound, despite the misgivings of all who have known the Monger’s past. Willard turns his life over to Christ. The feds are swarming around the tribal home, hoping to capture Zeke when he arrives for the funeral.
Zeke decides to use the government and media attention to God’s advantage. He, Doc and Bob attend the funeral. They not only have the opportunity to clear their names, but they’re able to share the message of Christ with millions through television.
Williard is reunited with his beloved aunt who has prayed for him for many years. After questioning and a night of lockup, Zeke, Doc and Bob are freed. The media reveal that Operation Dry Bones, based on the feds’ accusations that the Holdouts were murderous and intolerant, was baseless.