The Prophecy

Thomas Dagget, a Catholic seminary student, loses his faith when he sees disturbing visions of a war between angels. Years later, Thomas is a detective with the Los Angeles Police Department. Two angels fall to Earth: one, Simon, enters Thomas' home and warns him of coming events, before disappearing. The second, Uziel, a lieutenant of the angel Gabriel, is killed in an altercation with Simon. Investigating the disturbance, Thomas finds in Simon's apartment the obituary of a recently deceased Korean War veteran named Colonel Arnold Hawthorne and the theology thesis about angels which Thomas himself wrote in seminary. Meanwhile, in Chimney Rock, Arizona, Simon finds the dead veteran awaiting burial and sucks the evil soul out of the body.
The medical examiner informs Thomas that Uziel's body is like nothing he has seen before: it has no eyes, no signs of bone growth, hermaphroditism, and the same blood chemistry as an aborted fetus. Among the personal effects found on the body is an ancient, hand-written Bible, which includes an extra chapter of the Book of Revelation that describes a second war in heaven and prophecy that a "dark soul" will be found on Earth and used as a weapon.
Unknown to Thomas, Gabriel arrives on Earth. Needing a human helper, Gabriel catches Jerry, a suicide, in the moment of his death and keeps him in a state of limbo. Unhappily dominated by Gabriel, Jerry retrieves Uziel's belongings from the police station while Gabriel destroys Uziel's body in the morgue. After finding Hawthorne's obituary, Gabriel and Jerry head for Chimney Rock. Before Gabriel arrives, at the local reservation school Simon hides Hawthorne's soul in a little Native American girl, Mary, who immediately falls ill and is taken care of by her teacher, Katherine.
After finding Uziel's burnt body, all evidence of its oddity now lost, Thomas hurries to Chimney Rock. When Gabriel realizes Hawthorne's soul is missing, he confronts Simon. Gabriel says Hawthorne's soul will tip the balance to whichever side possesses it. Should the rebellious angels win, Heaven will become like Hell with earth in its thrall. Simon refuses to reveal its location, and Gabriel kills him, ripping out his heart. Mary shows signs of possession by the evil soul; she suddenly recounts an incident from Hawthorne's harrowing war experiences in first-person perspective. Meanwhile, Thomas examines Simon's remains and questions Katherine. In Hawthorne's home, he finds evidence of war crimes. Thomas visits a church to reflect and is shaken by a verbal confrontation with Gabriel. He is beginning to understand the nature of the jealous angels who hate humans because God loves them most.
At school, Katherine finds Gabriel questioning the children. After he leaves, she rushes to Mary's home and finds Thomas there. As Mary's condition worsens, Katherine takes Thomas to an abandoned mine where she had seen Gabriel. Inside, they find angelic script and experience together a terrible vision of the angelic war. They rush back to Mary's home, only to find Gabriel and Jerry there. Thomas kills Jerry, who thanks him for the release. Katherine stops Gabriel temporarily when her wild gunshot misses him and blows up Mary's trailer home. The three protagonists flee to a Native American site where Mary can be exorcised. In a hospital ICU ward, Gabriel recruits a new unwilling assistant, Rachel, just as she dies of a terminal illness. He needs her because he doesn't know how to drive.
That night, Lucifer confronts Katherine and tells her that "other angels" have taken up this war against mankind, and since then, no human souls have been able to enter Heaven. He knows of Gabriel's plot to use Hawthorne's soul to overthrow the obedient angels, and he knows that if Gabriel wins, under his influence Heaven will ultimately devolve into another Hell. That's unwanted competition. The next day, Lucifer appears to Thomas and advises him to use Gabriel's lack of faith against him. Gabriel arrives and attempts to disrupt the exorcism ritual. Thomas kills Rachel, and he and Katherine fight Gabriel.
Lucifer appears first encouraging the tribe to complete the exorcism. Then he confronts Gabriel telling him that his war is based upon arrogance, which is evil, making it Lucifer's territory. Gabriel taunts Lucifer about his past when he fell from grace; Lucifer tells Gabriel he needs to go home and rips out his heart. Simultaneously Mary expels out Hawthorne's soul, a rancid cloud of evil. The "enemy ghost" starts to attack the people but a bright light from Heaven immediately destroys it. With the threat to his evil kingdom eliminated, Lucifer tells Thomas and Katherine to "come home" with him. They staunchly refuse. "I have my soul...and my faith," declares Thomas. Lucifer drags Gabriel to Hell. As morning comes, Thomas comments on the nature of faith and what it means to truly be human.

Question: Who's soul is missing?
Answer: Hawthorne's soul is missing and Gabriel is the one who discovers it.