Paul Callan works as an investigator of miracles for the Archdiocese of Boston. Growing weary of his job and the tests it places on his faith, he takes a leave of absence and travels to Arizona to work on an Indian Reservation.

While there, Father Calero calls him and asks him to investigate a young boy, Tommy Ferguson, who supposedly has the power to heal others. Skeptical at first, Paul meets with Tommy and witnesses his abilities. He discovers that the young boy is dying, and that every time he heals another, his own health deteriorates. He also learns that his path and Tommy's are somehow inexorably linked.

When Paul is in a potentially fatal car crash, Tommy uses his power for the last time, and gives his own life to save Paul. As Tommy heals him, Paul sees the words, "God Is Now Here" written in his own blood.

His faith renewed, Paul returns to the church but the Monsignor dismisses his findings, causing him to resign. Paul is then approached by a stranger named Alva Keel who tells him that he is not alone in his experience. There have been 6 others who witnessed hemography, but they instead saw the words, "God is Nowhere." Keel urges Paul come to work with him at Sodalitas Quaerito, an organization devoted to searching for the truth.

Sodalitas Quaerito is called in to investigate when a commercial airliner disappears for one minute and four seconds. In that missing time, each passenger experienced a different phenomenon and is now inexplicably altered by the event. They interview, among others, a child who has seen her own bleak future, a paralyzed woman who has regained her ability to walk and talk, and a flight attendant who is now speaking in tongues and lecturing on the physics of world destruction. They realize that each person has come to manifest whatever was on their mind at the moment that the plane disappeared. However, after only a few hours it becomes obvious that these visions and abilities are fading. Paul tries desperately to reunite the crippled woman with her husband while she can still talk, but the authorities thwart his every attempt and he is forced to watch as she returns to a vegetative state. In a poignant final scene, Paul brings a stolen interview tape to the woman's husband so that he can hear what she had wanted to tell him.

A doctor's work with a patient suffering from a paralyzing disease yields unusual results when it appears that the patient can suddenly communicate through his computer. The patient, Sherwood Nichols, displays remarkable abilities and knowledge about curing the disease. The doctor's daughter, Raina, is both intrigued and alarmed by these findings, and enlists Paul's aid in discovering the truth about what it going on. Paul and Alva determine the patient is possessed by an entity, a demon who calls himself "Mr. Friendly". In the guise of Sherwood, this creature convinces the doctor to knock Paul out and overdose the other patients. Alva shuts down the patient's life support long enough to drive the entity out. Later in the hospital, the doctor reveals that his desperation to cure the disease resulted from Raina's death of the same disease two years earlier.

Paul is shaken when a bus explodes after he sees the visage of a young girl aboard. After the tragedy, Paul learns that the unidentified body of a small girl is being held in the local morgue. The body is amazingly without any scars or evidence of the explosion, although he is certain that she is the girl he saw. Soon another disaster occurs, also accompanied by a vision of the girl and another identical unclaimed body. After further visitations and tragedies, Paul realizes that the girl's ghostly appearance is causing these catastrophes and he searches for a way to placate the disturbed spirit. The investigation leads the team to Rosanna Wye, the now aged mother of the young girl. The telling of her story and their ultimate reunion finally puts the little girl's spirit to rest.

After receiving a terrified confessional phone call from a small town in Michigan, Sodalitas Quaerito sets out to uncover the truth behind several mysterious murders. Upon arrival, Paul immediately makes contact with a troubled young man, Travis, who believes that he is the cause of the violent deaths. Paul learns that his father is none other than the town Sheriff, whose abusive treatment of Travis' late mother led not only to her death, but also the death of Travis' unborn twin brother. With the assistance of Alva and Evelyn, Paul discovers that the entity responsible for the brutal murders is not Travis, but the spirit of his brother, punishing those who failed to protect Travis from his abusive father. Paul tries to warn Travis' father of the mystical threat but only his death sets Travis free from his brother's ghostly wrath.

Paul comes under investigation by the police after a woman is found murdered in her home, leaving behind her diary where she had sketched his name and image, along with the words "God is nowhere". Shocked by this irrefutable reference to his own paranormal experience and unable to get a straight answer from Alva, Paul breaks into the locked files on hemography and discovers that three other individuals who experienced the same phenomenon have also been murdered. Angry with Alva for keeping such vital information secret, Paul sets out on his own for Denver to warn a fifth person, a woman, of the unknown threat. Before he is able to reach her, he is apprehended by the police and taken in for questioning. While there, he receives word of her murder. Paul is released from custody, and goes to find the killer's final target, a man living in Oregon. Paul hurries to the man's house where both he and the intended victim are accosted by a boy, Chad Goodwell. He is shocked to learn that this young man has also been visited by Tommy Ferguson, and that a voice he believes is God, has sent him on this holy crusade the wipe out the evil that was his past victims. Before killing himself, Chad tells Paul "it's up to you now".