In 1980, Lee Strobel (Mike Vogel) is an award-winning investigative journalist for the Chicago Tribune, who has just been commended for his work on investigating the Ford Pinto fires. One night, Lee, his pregnant wife Leslie (Erika Christensen) and their young daughter, Alison, are out to dinner when Alison begins choking on a gumball. A nurse named Alfie (L. Scott Caldwell) comes to Alison's aid. After helping Alison spit the gumball out, Leslie thanks her for saving her daughter. Alfie replies that it wasn't her, but it was Jesus that saved her. Alfie explains that she is a nurse at the local hospital and that she and her husband were supposed to go to another restaurant that night, but she got a feeling that she was supposed to come to the restaurant that they were at that night.
Later that night, Alison asks her mom and dad about who Jesus is. Leslie tries to explain it to her, but Lee says that Jesus is a story that a lot of people tell like the storybooks that he reads to her at night. After Alison goes to sleep, Leslie tells Lee that she thought that they weren't going to force their beliefs onto Alison and that they were going to let her make up her own mind. Lee doesn't want to go into it, and they let it go.
The next day, Leslie goes to see Alfie to thank her again, and Alfie invites Leslie to her church. Leslie goes, and after the service, she talks with Alfie in her car. Alfie asks Leslie about Lee and what he believes. Leslie says that Lee only believes "in the facts." Leslie goes to Alfie's church again on another night, and when she gets home, she tells Lee that she went to see Alfie the other day to thank her and that Alfie invited her to her church and that she went. Lee says that he wishes he could have been there to see that. Leslie tells him that she wanted to go and that she went again and that time, she says that she felt something more real than anything she's ever felt in her life. After hearing that, Lee storms off and tells his wife that he's going out to file a missing persons report, to which Leslie replies that that is not funny. Lee says it is not meant to be.
Lee decides to put his investigative skills to the test to prove that Christianity is a hoax. He talks to Religion reporter, Kenny London (Mike Pniewski), who tells Lee that the Christian faith hinges on the resurrection of Jesus Christ and that if that were proven to be false, then everything would fall like a house of cards. So, Lee goes and sets up an unused room in the basement of the Tribune to gather evidence to disprove the resurrection of Jesus.
Lee goes to talk with a leading expert on the resurrection. The man tells Lee that there are around 500 people who testified that they saw Jesus alive weeks after He was killed. After the meeting, Lee gets paged by Leslie, who has gone into labor and has given birth to their son, Kyle.
During this time, Lee is also investigating a shooting between a cop, Joe Koblinsky, and a young black man, James Dixon. Lee goes to see Koblinsky in the hospital, but Koblinsky won't talk to him, except to tell Lee to write a story that will put Dixon away for a long time. Lee finds out that Koblinsky has arrested Dixon over a half dozen times previously and has concluded that Dixon is Koblinsky's informant. Lee meets with another cop to try to get confirmation that Dixon is Koblinsky's informant. The cop confirms Lee's suspicions and Lee runs the story.
Meanwhile, Lee meets with an agnostic psychologist, Dr. Roberta Waters (Faye Dunaway). Lee presents her with his idea that maybe the 500 people who saw Jesus alive after He was crucified, maybe they were seeing a hallucination. Dr. Waters says that a mass hallucination where 500 people saw the same exact thing and/or person, would be an even bigger miracle than the Resurrection itself. Dr. Waters asks Lee about his relationship with his father, Walter (Robert Forster). Dr. Waters asks Lee if his father was cold and distant towards him growing up. Lee says that he was. Dr. Waters tells Lee that all of the most well-known atheists (e.g. Sigmund Freud) all had a father that either died when they were young or were abusive in some way towards them. She calls it a "father wound."
After Lee's story, regarding Dixon being an informant, is published, Dixon is sentenced to 15 years in prison after pleading guilty. At the trial, Lee asks Dixon why he pled guilty since earlier in the film, Dixon told Lee that he was innocent. Dixon tells Lee it was because his story left him no choice. Koblinsky goes to see Lee after the trial and thanks him for the story that he wrote. Lee sees that Koblinsky's arm is in a sling. Koblinsky tells Lee that it is because he still has bullet fragments in his spleen.
Lee starts to think about that and looks at the crime scene photos of Koblinsky's wound. He talks with Dixon's attorney, and they go to the evidence lockup to look at the evidence taken from the scene. Lee notices that if Koblinsky got shot and had bullet fragments from his spleen, he would have been shot from a downward angle. Lee sees another photo of Koblinsky with a pen in his pocket. Lee finds the pen among the evidence and opens it to find a homemade pen gun, with a bullet casing inside. The casing matches the bullet extracted from Koblinsky. Dixon's attorney explains that pen guns are illegal for a police officer to carry. They conclude that Koblinsky's pen gun went off in his shirt pocket and instead of admitting that it was because of the pen gun, Koblinsky reported that Dixon shot him.
Lee goes to his editor (Frankie Faison) to explain that Koblinsky played him. His editor tells Lee that he let himself be played and has risked the reputation of the paper and a retraction has to be printed now. Lee tells his editor that he is going to be taking a few personal days off. During these personal days off, Leslie gets baptized. Angry, Lee goes and gets drunk. When he comes home, he gets into an argument with Leslie and ends up yelling at Alison. Later on, he goes to apologize to Alison, but she ignores him, feeling heartbroken.
The next morning, Lee gets onto a plane to Los Angeles where he goes to consult with a medical doctor about if Jesus did die on the cross or if he just passed out and people assumed he died. Lee talks to Dr. Alexander Metherell (Tom Nowicki), and the doctor calls Lee's theory rubbish. Dr. Metherell asks Lee if he knows what happens in the flogging that Jesus endured. Lee assumes it is just a whipping with a lash. Dr. Metherell explains that a flogging was a brutal beating with a spiked weapon that would have left Jesus in near-critical condition from blood loss. Then being nailed to the cross, He would have had to lift himself up repeatedly, in order to draw his next breaths, since his chest was constricted and would die from asphyxiation if He did not do so, which is what He does eventually die from.
Then, after He is dead, when He is stabbed in the side by a Roman guard, Jesus bled water and blood, which is proof that He died from asphyxiation. Dr. Metherell says that if Lee doesn't believe him, would he believe the opinion of the American Medical Association, which Lee says he would. Dr. Metherell hands Lee a copy of an issue of the American Medical Association Journal, which states that conclusive evidence has shown and has been proven that Jesus Christ did die on the cross.
Shortly after Lee leaves the meeting, Leslie calls him to tell him that his father has passed away. Lee goes to the funeral and afterward, goes to his parents' home. He looks through his father's wallet and finds an article that was written about Lee joining the Tribune. When his mother walks in, Lee asks her if she knew he had that in his wallet. She says that he did. She hands Lee a photo album with cutouts of all of Lee's articles since he was writing for his school paper. She tells Lee that even though he didn't show it, his father did care about him. Lee heads home from the funeral with his family, when he hears the news that Dixon was beaten up in prison and that he is in critical condition at the hospital. Lee goes to see him at the hospital and apologizes to him for what he and his story did. Dixon tells Lee that it was because he (Lee) did not want to see the truth.
Lee goes back to the office. At the end of the night, as most everyone has gone home, Lee berates Kenny for being a Christian. Kenny rebuffs Lee saying that Lee is supposed to be this hot-shot, golden boy reporter and yet is having trouble accepting the facts when his job is all about reporting the facts. Kenny tells him to suck it up and report the facts. Lee goes downstairs to his reporting room and looks over all the notes from all the interviews that he has done about the resurrection. Finally, he accepts the truth, saying "Okay, God. You win."
Lee goes home and talks to Leslie, telling her that when she became a Christian, he freaked out and made it his mission to disprove her faith. He tells her that God did not give up on him and neither did she. He tells her that he believes too. They hug, and he prays to God. Three months later, Lee goes to talk to his editor to pitch him an idea for an article on his (Lee's) journey from atheist to believer, but his editor does not agree to it since it would jeopardize the credibility of the paper. Later on, Lee tells Leslie about it, and Leslie recommends that Lee write a book about it.
In the final scene, Lee goes to his typewriter and titles the book "The Case for Christ."
The epilog shows that Lee became a best-selling author and that both his children have become the writers of Christian books too. Lee is now a professor, living in Texas and travels to different places, sharing the story of his journey.
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