It's a week after the rapture and the millions of people who vanished into thin air are still missing. Chaos rules the world as panic and grief-stricken survivors continue to search for their lost loved-ones. Suicide rates are skyrocketing, businesses and homes are being looted, and martial law is in effect. A desperate world looks to the leadership and guidance of UN Secretary General Nicolae Carpathia, the only person offering any answers, hope, and plans to restore peace and order.
While Carpathia has the world's adoration and trust, he is seemingly unaware of a small group of rebels spreading the truth that he is in fact the Antichrist. Buck Williams (Kirk Cameron) is a highly respected television journalist who has seen firsthand Carpathia's manipulative and deadly powers. His position allows him special access to a global audience through the media and to Carpathia himself. Airline pilot Rayford Steele (Brad Johnson) and his 20-year-old daughter, Chloe (Janaya Stephens), make up the rest of this group. Ray is still struggling to come to grips with the loss of his wife and son, but his recent salvation and friendship with Pastor Barnes have brought him back to the church and closer to his feisty daughter. Ivy Gold, Buck's assistant from the first film, comes into the GNN headquarters, and they go to Buck's apartment so they can work on the story of the vanishings.
As the Tribulation Force struggles to open the eyes of the world to the truth, Global events get even stranger when word leaks out that three men have mysteriously burned to death at one of the holiest sites in Israel: the Western Wall. At the same time, Rabbi Ben Judah, one of the leading religious scholars of his time, plans to make a world-altering announcement based on years of research. Pastor Barnes believes both events are linked to Carpathia, signaling the oncoming terror of The Tribulation. He acts quickly by getting Ray and Buck to embark on a dangerous mission to infiltrate Carpathia's organization. They must get to Ben Judah before he makes his announcement. Buck is going to the Wailing Wall to get the witness on tape, but Steve Plank tries to talk him out of it. Bruce wants Rayford to join Carpathia's staff as the pilot of the new plane that the US government gave to Nicolae. Rayford initially turns down the mission.
Rayford, while grieving about his family, receives a call from Chris (his former co-pilot). He goes to Chris' apartment, and saves Chris' life and soul, because Chris wanted to commit suicide. Rayford then accepts Bruce's mission, to spy on Nicolae. Chloe is concerned for Buck and Rayford, but Buck starts to care for Chloe.
Rayford then heads to Hattie to try and fly the plane. Initially, Hattie is suspicious of Rayford (due to their last confrontation), but Rayford convinces her that he is the right man for the job. Meanwhile, Chloe goes to Bruce and asks about relationships during this time of chaos. She then goes to Buck's apartment where she sees Ivy Gold, Buck's assistant. Ivy blows Chloe off, thinking that she is just some star-struck fan of Buck's. Buck tries to call the Steele's house, but Chloe doesn't want to chat with him. When Rayford finally picks up the phone, he uses a bit of deception to have Buck meet with Chloe. When Buck leaves his apartment, he is taken to the roof of his building where he has a meeting with Nicolae. Buck is granted access to the Wailing Wall, and he goes to meet with Chloe.
Chloe first blows him off, but some deception from Rayford gets them to talk. Buck and Chloe make up and start a relationship. Rayford and Buck then leave for Israel. Meanwhile, Ivy starts to visit Chloe at the church, initially to apologize for her behavior, and then later because she starts to become friends with Chloe and Bruce. Nicolae then ups the security at the Wailing Wall; and, with the help of Steve Plank, they create a "One World" religion. At the airport before leaving for Israel, Buck and Chloe share some time together. Rayford tells Chloe that he will watch over Buck.
On the airplane, Rayford attempts to find some solid evidence about Nicolae. He finds some information on a computer pertaining to Rabbi Ben-Judah. While obtaining the evidence, Nicolae comes in and congratulates Rayford on being the pilot. As Rayford hands Nicolae their ETA, he sees a vision that disturbs him. When on the ground in Israel, Rayford shows the email he downloaded from Nicolae's computer to Buck. They realize that the conversation about Ben-Judah was about the speech he was going to give. Steve and Nicolae changed the speech because Ben-Judah was going to announce Jesus as the Son of God. Instead, because of the new changes, Ben-Judah is going to announce Nicolae as the Messiah. Buck goes to meet Rabbi Tsion Ben-Judah. He asks the Rabbi to come and discredit the witnesses, and prove that Jesus is the messiah. He agrees. Nicolae puts added security on the wall, and Rayford and Buck pray to God to help the get message out.
They go to the Wailing Wall to meet the two witnesses. Rayford distracts the guards (through God's intervention in the form of an angelic singer) and Buck and Ben-Judah slip through to confront the two men. Ben-Judah chats with the two men and learns about Jesus. They are attacked by UN guards and the two witnesses breathe fire at their attackers and they die. During the broadcast, Nicolae cuts the feed right in the middle of the Ben-Judah/Two Witnesses confrontation. Buck then learns that the broadcast got cut and Ben-Judah ran off. Ivy comes to the church to give Chloe some food, and witnesses Chloe ministering to a severely burned fireman who then passes away. Ivy hugs Chloe, and states that the fireman was at peace. Chloe remarks that he found God.
Nicolae comes to the Temple Mount and speaks to the masses. Rabbi Ben-Judah then comes to the Temple Mount and starts giving his speech. Nicolae, along with his advisors, watch the broadcast. Rayford, in the cockpit, asks the copilot to take over. He then goes out and pulls the fuse to stop Nicolae from ruining the broadcast. Rabbi Ben-Judah then gives his speech about Jesus being the Messiah, and how he needs to be forgiven. Nicolae then orders the broadcast to be cut. In Chicago; Ivy, Chloe, and Bruce are watching, with Ivy crying. When the broadcast is cut, Ivy is stunned, but Chloe leads her to Jesus, with Bruce praying with them.
In Israel, Ben-Judah's announcement leaves the crowd mixed. Buck asks Ben-Judah if he will be ok, Ben-Judah states that Buck helped millions learn the truth. Back in the cockpit of the airplane, Rayford hangs up pictures of his wife and son. He is finally at peace about their disappearing.
Carpathia, filled with rage, tells God that it is his time to rule the Earth. Back in Chicago at the New Hope church, Bruce is leading worship. Ivy, Chris, Rayford, and Chloe are singing a hymn (How Great Thou Art) when Buck enters. Buck hugs everyone as they continue to sing.
A third and final film was added to the series in late 2005, titled Left Behind: World at War.
The film was nominated for "Best Live-action DVD Premiere Movie" by the DVD Premiere Awards and "Best Sound Editing" by the Golden Reel Award.