The movie opens up at an empty house. A phone has been dropped, with the dial tone still going, a pot is still cooking on the stove, a television is still on, indicating a person was still watching it, and clothes are still on the seat. Outside the scene is chaotic with a panicked mother frantically looking for her daughter and a man looking for his wife after a car crash.
The movie switches to the house of Adam Riley (White), who is visited by his friend Charles Baker (Downes). They are FBI agents working at the same field office. At the FBI headquarters, agents are briefed and are given an assignment, a folder containing names, and told to interview the relatives of the missing people. These include Mr. Fulton, a live in nurse named Peggy, and Katherine, George’s wife (whose two kids Troy and Tanya are also among the missing). As they are leaveing, Charles is called back to the emergency room when finds that his wife has miscarried.
A Jewish rabbi named Jacob Krause (Brad Heller) is at Synagogue performing a ritual, and picks up a Bible upon hearing the news report on the radio. Jacob suddenly pick up residence in an abandoned Christian homeless shelter, (later he is closed down and has continually run ins with the military).
Katherine at the hospital is told that four months have passed and she has shown improvement in her performance. While waiting outside on a bench, Krause comes and preaches the Word of God.
The President makes a State of the Union speech, addressing the recent events. He then informs of a One World Currency and the installation of a B-chip, which is implanted through the palm and “acts as a credit card”. Just when Adam and Charles are close to finding answers to the puzzle, the President orders all FBI agents to be taken off the case. Adam and Charles are given the task to capture Krause, considered to be a “dangerous criminal”.
Adam and Charles proceed to Krause’s last known location, but the only evidence they find is a picture. An argument erupts between them leading Charles to drive home. Later that night, Riley goes to see Dr. Wilkins at his church. He asks him about his theory of the rapture, mentioning a debate between him and two scholars on television. Wilkins correctly deduces that Krause is one of the 144,000 who will convert those left behind to God himself.
Adam and Charles go back to Krause’s location, and Charles is angry that Riley is going on a “hunch” based on the picture. He then reveals some writing on the back, and that the message was for him to find: SEEK, AND YOU SHALL FIND. However, on their way, they meet up with the military as Riley squares off with Lt. Fredricks (Monte Perlin). They discover that the military has captured Katherine, and Adam breaks her out. She is soon discovered and a standoff occurs at a diner. Katherine has both agents lower their weapons and says she’s ready and that God will be there to protect her. She sings as the military leave the diner, but not before Fredricks threatens Adam.
Adam and Charles arrive at the mountaintop where they discover Krause alone. Adam tells him to go easy on Krause, however Charles arrests Krause at gun point, citing his orders. Krause is able to convince Adam, but not Charles, that the “B” in the B-chip stands for Beast and that the Gospel of Jesus Christ is true. They stop at a local gas station, where Adam fills up the gas tank while Charles goes inside. Krause finally gets Adam to believe in God, and helps him out in his escape. He drives the car off, leaving Charles there. Charles calls Adam’s cell, and after getting a nonsensical answer from him, borrows a car. The military blocks Adam’s car from proceeding further. The guard checks Adam's ID, but reveals it has been blocked. Before Adam could proceed further, Charles stops him and convinces the military he’s harboring a fugitive. When they look in the trunk of his car, they find nothing. Charles knows Krause was released, and Adam is taken to prison by the military.
The final scenes show Charles packing his stuff at his desk, indicating he was fired, and Adam receiving his dinner from a fellow prison guard Adam takes the bread, and finds a piece of paper with bible passages. He goes to the window with his arms spread out. Krause goes back up to the mountain, indicating that his journey is far from over.
