A team of Vatican sponsored mercenaries led by Jack Crow (Woods) rids an abandoned house of vampires in the middle of New Mexico. The sun sets and, as the Slayers leave, the Master bursts out of the ground outside the house.
The slayers stay at a motel in the middle of a desert, getting drunk, smoking and partying with women as they celebrate their victory. One of the prostitutes is a young woman named Katrina (Lee). When the master vampire, Valek (Griffith), turns up at the motel, he bites Katrina and massacres the slayers and prostitutes. During this attack Valek sees Jack and calls him by name which astonishes Crow. Crow and his partner, Tony Montoya (Baldwin), run outside and grab a weak and nearly unconscious Katrina, take a pickup truck and drive off. Valek catches up with them, jumps on the back of the truck, but is shot in the face and this knocks him off the vehicle and onto the road.
Narrowly escaping from Valek, they keep on driving for a few more hours until dawn and narrowly avoid hitting a stalled vehicle in the road. They walk east, coming to a gas station. They steal an automobile at gunpoint. While Crow goes back to the motel to deal with the remains of the team and prostitutes, Montoya takes Katrina to the nearest hotel. Crow stabs the corpses of his fellow slayers and the other victims in the heart with a wooden stake, then beheads them to prevent them from turning into vampires. Crow then burns down the motel and buries the heads in the desert. Meanwhile, Montoya has gotten another hotel room and he tells Katrina that she has been bitten by Valek and that she too will be one soon if they cannot find and destroy him. She now has a telepathic link to the Master.
Jack meets his boss Cardinal Alba (Schell) who introduces him to Father Adam Guiteau (Tim Guinee). Jack reports that his entire team has been destroyed and that only one vampire did this. Cardinal Alba and Father Guiteau show Jack a centuries-old painting of a man which turns out to be the master vampire that attacked and killed Jack's crew. He was the first documented case of vampirism and is most likely the progenitor of all vampires. Jack is told that he will wait for his new team to get in before he hunts down Valek but that Father Guiteau would be replacing the priest that was murdered at the hotel.
Meanwhile, Katrina tries to escape as Montoya rests. He awakens and grabs Katrina, pulling her through a window and back into the room. Katrina sees a cut on Montoya's arm and her vampire instinct takes over as she grabs it and bites him. He then uses a Zippo cigarette lighter to burn the wound clean. Jack and Guiteau get to the hotel where Montoya and Katrina are holed up. Katrina awakens having linked to Valek and Jack gets her to tell him what's going on. She has a vision from Valek's point of view which shows a sign that says San Miguel and Jack tells Guiteau to call all the churches in that area asking of any are missing any old priests. Soon after, Katrina loses the connection to Valek but Guiteau finds a lead.
Jack tells the priest some of his past, about how his father was bitten by a vampire, killed his mother, came after Jack and that he killed his own father. He then asks what it is Valek's after and Guiteau tells him that he wants an ancient relic called the Black Cross of Berziers and that Valek was once a priest who was thought to have been possessed by demons. The Bérziers Cross was used in an exorcism that was cut short but the result was that Valek was forever changed into the first vampire and that the priest Valek killed was the only person who knew of the location of the Cross. Jack and the rest head to the old priest's church to try and see if they can find out the location of the Berziers Cross now that Valek has had to stop at sunrise.
The next night Valek rises, with seven companions. Through Katrina's link to him, the Slayers learn that the seven other vampires are Masters as they converge on an old Spanish mission and soon Valek has the Cross in his possession. The next day, Jack and the others find the Spanish mission and Guiteau tells them that Valek wants the Berziers Cross to complete his exorcism which was cut short the first time. Completing the ritual would supposedly make him able to walk in the daylight and that would make him unstoppable. They then travel to a nearby town that seems to be deserted.
The security cameras in the town jail are still on and Jack spots one of the Master vampires walking around. Montoya stays outside and works the winch attached to the Jeep, keeping an eye on the continually weakening Katrina while Jack stays on the ground floor to shoot them with his crossbow leaving Guiteau to be the bait to lure them to Jack. They manage to get a couple of the Masters but not before the sun sets enough for Valek and the other Masters to come out as well as the town's missing population who have been turned into weaker vampires. Guiteau manages to find a place to hide without being seen, but Valek and the rest get hold of Jack knocking him out.
Montoya and Katrina escape, but as the sun sets Katrina fully turns into a vampire and bites Montoya on the neck. He makes no move to stop her and she then starts walking back to the town, now a member of the undead. When Montoya awakens, he loads a submachine gun and fires a volley and smashes the hot barrel against the open wound on his neck. Jack awakens to find that he's been tied to the front of his truck and that he's surrounded by the recently turned towns folk, the Masters and Valek. Cardinal Alba has betrayed the Vatican Council, explaining to Jack that he's planning on reproducing the first exorcism (which requires the blood of a crusader: Jack's, climaxing with his crucifixion on a burning cross) and becoming Valek's first "new child." The exorcism must be completed by dawn. Katrina walks back into the town and the Cardinal begins the ritual.
Guiteau is hiding in one of the stores and finds a shotgun with shells under the counter. He gets up on the roof where he shoots and kills Cardinal Alba. Valek then tells Guiteau to finish the ritual and Guiteau refuses placing the shotgun against his head. Montoya's jeep comes into the town and he uses Jack's crossbow to shoot the cross that Jack has been tied to the cable. Jack is dragged behind the jeep. Valek tries to get the Bérziers Cross but the sunlight reflecting off of the jewels in the cross burns his hands and he can't get hold of it. He heads for shelter and Jack grabs the Berziers Cross and heads off after Valek. Jack and Valek face each other and Jack rams the cross though Valek's chest then throws himself through the support post for the roof causing it to collapse allowing the sun to get to Valek and he dies in a spectacular fireball.
Montoya gets the jeep and gets ready to leave only to be confronted by the shotgun-wielding Guiteau, knowing that Montoya is turning into a vampire. Jack gets Guiteau to agree to a two day head start as Montoya backed up Crow for two days after being bitten by Katrina. Crow and Montoya embrace like the brothers they became after Crow informs Montoya that after the two days he will hunt down and kill both of them. Montoya and Katrina leave and the movie ends with Jack and Guiteau heading off once again to the jail to kill the rest of the vampires that made it to shelter.