Around the world, unusual phenomena that resemble signs of the Biblical apocalypse begin to surface: a mass death of sea life in Haiti and a devastating freeze in the Middle East, and at each site a mysterious traveler arrives and opens a sealed envelope just before catastrophe. The Vatican tasks the Reverend John Heard with leading the inquiry, though he cautions that these events may be hoaxes or have scientific explanations.
In California, Abby Quinn, Demi Moore is pregnant and preparing for the birth of her child. Her husband, Russell Quinn, Michael Biehn, a defense lawyer, represents Jimmy Szaragosa, John Taylor, a man with Down syndrome charged with murdering his incestuous parents and claiming to have acted under God's command; Jimmy is convicted and sentenced to death.
For extra income, Abby and Russell take in a mysterious traveler who identifies himself as David Bannon, Jürgen Prochnow. He captivates them with stories of the Hebrew myth of the Guf (or Guph), from which souls come to earth, and how a sparrow is the only living creature that can see a soul as it leaves the Guf. Abby begins to have terrifying nightmares of a man like David being struck down by a Roman soldier, and the question "will you die for him?" is asked of her. She also experiences inexplicable physical reactions. She uncovers an ancient note that leads her to fear he intends to harm her child. When she confronts him, he says that God's grace is empty and soon no souls will be available for newborn babies. He is wounded when she stabs him, but he shrugs off the injury and says he cannot die again.
> cannot die again.
It becomes clear that he is the Second Coming of Jesus Christ. Abby's nightmares become visions of his crucifixion, and she learns that she is the reincarnation of Seraphia, the woman who offered Jesus water but was turned away by Cartaphilus, Pilate's porter. The signs of the apocalypse continue to unfold and trigger a giant storm. Abby teams up with Avi, a rabbinical student, Manny Jacobs who helps her interpret the symbols and prophecies.
Father Lucci, Peter Friedman, arrives in California as part of the investigation and is revealed to be Cartaphilus himself, cursed to wander the earth until Christ's return. He intends to let the apocalypse unfold to break his own curse. Abby flees with Avi's aid, and together they search for a Bible to learn what will come next. They discover that the sixth sign will be a solar eclipse expected the following day, and that the fifth sign — the torture and death of a martyr for God's cause — must occur soon. Abby realizes that clemency has been denied to Jimmy, meaning his execution will fulfill the fifth sign.
In a race against time, Abby heads toward the prison to intervene, but Lucci has already infiltrated the facility. He kills Jimmy and wounds Abby, and is taken away by guards. The eclipse begins as a catastrophic earthquake rocks the area. Grieving and frightened, Abby goes into labor, but the baby's heart stops beating, marking the seventh sign: the birth of a soulless child. Yet Abby experiences a final vision of Seraphia's past and Cartaphilus's question. She answers with resolve:
> I will die for him.
The act of faith culminates as the child touches her finger, and her soul seems to pass into the newborn.
In a moment of miraculous revelation, Jesus appears in the hospital and tells Russell that Abby's sacrifice has refilled the Hall of Souls, ensuring humanity's continued survival. He instructs Avi to record this event for future generations.
