The third film in the Apocalypse series, about life during the Christian End-times
Helen is captured by O.N.E. and placed in the Day of Wonders program, but she recorded her conversation with Macalousso before he executed her. Tom reunites with Suzie, and she and the resistance successfully uplink Helen's video, and it's seen around the world. Tom and Jason both become believers.
Set before the events of the first film, Tom Canboro (Gary Busey) is a police detective investigating a man who attempted to kill his wife because she is a Christian before killing himself. During his investigation, he learns that at the same time of this attack, his brother-in-law Jason (Howie Mandel) attempted to kill Tom's sister Eileen (Margot Kidder) for the same reason, but his suicide attempt failed. At the hospital, Jason tells Tom that his mind was taken over by Franco Macalousso (Nick Mancuso), the President of the European Union, and was directed to kill Eileen. Since Jason has a history of mental illness, Tom doesn't believe him. But those beliefs change as soon as Tom sees several men come into the hospital with guns looking for Jason. These men are associated with Macalousso, and they did indeed use mind control on several random people who are associated with Christians. These test subjects were instructed to kill Christians then themselves, but Jason's survival potentially exposed their plan. The gunmen are to kill anyone who might have heard Jason talk about having his mind controlled, including Tom. After getting Jason to safety, Tom flees the hospital, but his car is taken over by the men via mind control, causing it to crash and putting Tom in a coma.
Tom wakes from his coma several years later, and he learns from his hospital roommate that the rapture has occurred. Franco Macalousso claims to be the Messiah, and One Nation Earth, or O.N.E., is making people choose whether to worship him or die. This is done through the Day of Wonders program that was begun some time ago after a delay (the events of the second film). Everyone who agrees to follow Macalousso comes out wearing the mark of the beast (a "666" on their hand). O.N.E. learns that Tom is now awake and plans to put a helmet on him, but he escapes from the hospital. Tom then goes into town, but quickly learns that without a mark, he is presumed to be a hater (what people call Christians) and is constantly threatened. He goes to his home, but it's empty. However, his police weapons are still there and he collects them, not realizing that O.N.E. is still pursuing him.
While all this is happening, there are a group of people attempting to tell the truth about Macalousso by uplinking Christian videos during Macalousso's speeches. Helen Hannah (Leigh Lewis), the former WNN anchorwoman seen in the first two films, is the head of this resistance group, and Tom's wife Suzie (Sherry Miller) is part of it. During one broadcast they interrupt, we learn that Thorson Stone, Jeff Fahey's character from the second film, was captured and executed. While uplinking a video to interrupt another broadcast, Helen is captured by O.N.E. and taken to their headquarters. There, she is forced to wear a Day of Wonders helmet, and comes face to face with Franco Macalousso himself. He tells Helen that he wants as many people to take the mark, because everyone who does is one less person that God can get for Himself. Macalousso doesn't care about the person, just their souls. He gives her one last chance to take the mark, and she refuses. He then straps her into a guillotine and beheads her.
Tom tracks down his brother Calvin (Joseph Ziegler), and asks about Suzie, Jason, and Eileen. Calvin says that both Suzie and Jason are nowhere to be found, but they don't have a sister. Tom then notices that Calvin has the mark on his hand. He then sees a pile of dynamite in the house, and Calvin tells him that he plans on blowing up every church in the city, killing as many haters as possible. Calvin then grabs a nearby helmet using mind control. Tom asks how he did that, and Calvin tells him that the Day of Wonders will release God-like powers buried inside him that God had no intention of ever sharing. He tries to put the helmet on Tom, but he knocks him out and flees. Tom then remembers a tree in the nearby park that he, Calvin, and Eileen all went to as kids. He goes there, and finds Jason. He tells Tom that Eileen disappeared during the rapture, but Suzie is alive and unmarked. They initially believed Macalousso's claims that he was the Messiah, but when they saw what was happening to those who were marked, they went into hiding. Jason also learned that when someone takes the mark, they lose all memory of anyone taken in the rapture, and that's why Calvin said they didn't have a sister.
Tom leaves Jason at the park and goes back to Calvin's house to try to talk sense into him, but he was killed for letting Tom get away. O.N.E. is still there looking for Tom, but they don't see him. Tom does hear them say that they found the source of the uplinks, and it's at Tom and Suzie's lake cottage. They also have a signal jammer that will prevent any illegal signal from being broadcast. After they leave, Tom collects the dynamite, meets back up with Jason, and they head to the cottage. Once there, Tom reunites with Suzie, and tells them that O.N.E. is on their way. But before they can do anything, an O.N.E. agent shows up. He asks everyone if they are ready to die for God, and they say yes. He then reveals himself as a resistance member working undercover in the O.N.E., and that was a test to ferret out any spies. He tells them that Helen is dead, but he has a video she was able to record from inside the Day of Wonders program. She intentionally allowed herself to be captured so she can get Macalousso to reveal himself as the Anti-Christ. The camera was embedded on her contact lens, and she was somehow able to get the video out to the resistance before she was killed.
O.N.E. arrives at the cottage, but Tom parked his car at a neighbor's house, so they think he is there. They go in with guns blazing, but they shoot Calvin's dynamite that Tom planted there, blowing up the house and killing all of the O.N.E. agents. The jammer is also destroyed in the blast, so the uplink can proceed without interruption. The speech that Macalousso is giving at that time is interrupted by Helen's video. When it finishes, Macalousso tells the audience that it's just another hater lie and to ignore it, but he can sense that the viewers are turning off the speech and he gets angry at the world.
The movie ends at a nearby church. Tom had once promised Eileen he would go to that church with her one day. Even though she is gone, Tom enters the church and prays to God and becomes a believer. Jason also goes to the church and tells Suzie that he too is now a believer.