The film opens with a bloodied and terrified priest slowly making his way across an ancient battlefield full of the bodies of thousands of dead soldiers. The priest reaches the dead body of another priest and tries to take a small demon idol of the head of Pazuzu from his hand, but suddenly, the dead priest briefly comes back to life and stops the living priest from taking it. The camera pulls back to reveal that the entire valley is littered with dead soldiers, many of whom have been crucified upside down.
The film then cuts to Cairo, Egypt in 1949, where the young Father Lankester Merrin (played by Skarsgård, who played the same part in Dominion: Prequel to the Exorcist) has taken a sabbatical from the Church and devoted himself to history and archaeology as he struggles with his shattered faith. He is haunted especially by an incident in a small village in the occupied Netherlands during World War II, where he served as parish priest: near the end of the war, a sadistic Nazi SS commander, in retaliation for the murder of a German trooper, forces Merrin to participate in arbitrary executions in order to save a full village from slaughter.
After World War II, Merrin is an archaeologist in Cairo, when he is approached by a collector of antiquities named Semelier who asks him to come to a British excavation in a valley called Derati in the Turkana region of Kenya. This dig is excavating a Christian Byzantine church built circa 500 A.D. — long before Christianity had reached that region of Africa. Semelier asks Merrin to recover an ancient relic of a demon, thought to be in the church, before the British can find it; small head of the Pazuzu idol. Merrin agrees and travels to the dig site. He is joined by Father Francis, a Vatican scholar who was on his way to do missionary work in East Africa but was diverted by the Vatican to ensure the church is not desecrated.
Upon arriving at the site, Merrin meets Major Granville, the British military officer in charge of the dig. Merrin also meets the chief excavator, a brutish man named Jefferies with visible boils on his face. He also meets Sarah Novak, a doctor who spent time in a concentration camp during World War II and is haunted by what happened to her there. Merrin's translator and guide is Chuma. In addition, Merrin learns that the diggers are disappearing or leaving in droves because the local tribesmen fear the church is cursed. Merrin witnesses a digger inexplicably experience a seizure.
Merrin visits the dig site. Only the dome is uncovered; the rest of the church is buried beneath the earth. Merrin discovers that the church is in perfect condition, as though it had been buried immediately after its construction were completed. Merrin, Francis, and Chuma enter the church through the dome. They find it is near-pristine condition, but there are two oddities. First, all of the statues of the angels holding weapons are pointing the spears downward, whereas it is conventional for statues of angels to either have no weapons or to point them triumphantly toward heaven. Merrin and Francis deduce the sculptors were trying to depict the angels restraining something that was beneath the church. The second disturbing discovery is that someone has vandalized the church by ripping the enormous crucifix from its place on the altar and suspending it with Christ on the cross in an upside-down position, which is considered a desecration.
Merrin is determined to learn more about the archaeological dig and asks to consult with the lead archaeologist, Monsieur Bession. Sarah tells Merrin that Bession went insane three weeks earlier and was transferred to a mental hospital in Nairobi. Merrin visits Bession's tent at the dig site and sees dozens of drawings of the same thing, the demon artifact the collector had asked Merrin to find. Merrin then travels to Nairobi to visit Bession, but when he enters Bession's room, he discovers Bession has carved a swastika on his chest and is speaking through demonic possession in the voice of the sadistic SS commander who tormented Merrin during the war. As Merrin registers these events, Bession slashes his own throat after saying he was "free." Father Gionetti, warden of the asylum, speculates that Bession was not possessed but rather "touched" by a demon, which drove him mad and eventually to suicide. Merrin is very skeptical, but before he returns to the dig site, Father Gionetti gives him the volume of Roman rituals to use in exorcism, although Merrin claims he will never use them.
Upon returning to the village, strange events continue. A local boy is attacked and killed by hyenas that seem to continuously stalk the dig, night and day. His younger brother, Joseph, enters a fugue state after watching his brother get ripped to pieces. The local chief's wife gives birth to a stillborn baby who is covered in maggots. Around the same time Merrin discovers a passageway leading to a cave underneath the church that houses an ancient pagan temple with the statue of the demon Pazuzu. He also finds evidence that this temple was used to conduct human sacrifices. Upon his return, he sees the local tribe cremate the stillborn baby. This makes Merrin suspicious, because there are stories of an epidemic that wiped out an entire village in the valley 50 years earlier. He had been told that the dead were buried in a graveyard just outside the valley. When he digs up one of the graves of the supposed victims of this plague, it is found to be empty.
Merrin confronts Father Francis about it, and Francis reveals to him the history of the Derati valley and the real reason he was sent there. He says that 1,500 years prior, a great army led by two priests came to the valley searching for the origin of evil. When they arrived in the valley, the evil presence consumed them and they killed each other. When the lone surviving priest made it back, Emperor Justinian ordered a church be built over the site, specifically the pagan temple, and then buried to seal the evil force inside of it. Father Francis reveals to Merrin that the builders of the church never meant it to be recorded in Vatican documents, however, a vague reference to it was recorded and found in 1893. Four priests subsequently came to Derati and enlisted the local tribe to help them. All of the tribesmen and the priests disappeared. The Vatican then ordered that the false graveyard be built and stories of a plague spread around to keep people away from the valley. Then the British just so happened to stumble upon the site. Francis then reveals that the Vatican sent him to see if the legend was true. When Merrin asks about the legend, Francis reveals that it is believed that the valley in Derati was the traditional spot of Lucifer's fall after the war in heaven.
At the end of the film, the dig's doctor, Sarah, turns out to be the possessed individual and has the demon exorcised from her in the tunnels below the church but dies. Fr. Merrin and Joseph emerge from the church, (once again buried in sand) and history has repeated itself. Everyone at the site was killed by an evil presence from the church, except for one priest. Now, only Father Merrin and the little boy are left as the British soldiers and the local tribes have annihilated each other. Merrin returns to Rome and meets with Semelier at a cafe, explaining he was unable to find the relic, Semelier replies, "But you found something....Didn't you?" As he leaves, Merrin is revealed to be wearing a collar and is now a priest again, having regained his faith in God, after defeating the demon with holy exorcism rituals.
John Frankenheimer was initially set to direct, but stepped down just before his death. He was replaced by Paul Schrader who aimed for a psychological film and delivered what he described as "footage without any of the bloody violence the backers had wanted." The producers were unsatisfied with the completed film Schrader presented them and fired him, replacing him with Harlin and hiring screenwriter Alexi Hawley to retool the previous script. Harlin re-filmed most of the movie, with some new characters added and others deleted. The character of Father Francis, originally played by Gabriel Mann, had to be recast with D'Arcy because Mann had a scheduling conflict. Izabella Scorupco replaces Clara Bellar in a retooled version of the doctor in the village. Though both movies center around Father Merrin's exorcism of a boy in Africa in 1948, little effort is made to be consistent with references in Exorcist II: The Heretic where Merrin is shown in flashbacks exorcising a teenage boy named Kokomu. In both Beginning and Dominion, the location and setting are different and the boy is not named Kokomu. In The Beginning, this boy is not present; a child appears to be possessed but it's not the same character as in Dominion and its a false lead.
The film is shot in Univisium (2:1) aspect ratio (developed by Vittorio Storaro, who also acted as the cinematographer), although the theatrical release was presented in 2.39:1.
After poor audience and critical response to Harlin's version, Morgan Creek gave around $35,000 to Paul Schrader to finish his version then allowed Warner Bros. to release Schrader's version theatrically under the title Dominion: Prequel to the Exorcist. It was released to limited showing in May 2005. It received slightly better critical reception than Harlin's version.
William Peter Blatty (the author/screenwriter of The Exorcist) said that watching Exorcist: The Beginning was his "most humiliating professional experience." On the other hand, Blatty said that Dominion is "a handsome, classy, elegant piece of work."
Critical responses to Exorcist: The Beginning were mostly negative, with the film earning a low 11% "rotten" rating on Rotten Tomatoes. Prominent critic Roger Ebert wrote, "I've seen both versions and much prefer Schrader's, and yet it must be said that Harlin did not prostitute himself in his version."
The project's estimated budget was $80 million ($30 million for Schrader's version and $50 million for Harlin's). Exorcist: The Beginning made $78 million at the worldwide box office.
Exorcist: The Beginning was nominated for two Golden Raspberry Awards, Worst Director and Worst Remake or Sequel, but lost to two other Warner Bros. films, Catwoman and Scooby-Doo 2: Monsters Unleashed, respectively.