An elite group of soldiers led by Mack (Cuba Gooding, Jr. ), are sent by a CIA agent named Elissa Cardell (Valerie Cruz) to rescue her father and scientist Wesley (Ron Perlman), who is working on an archeological dig site in the Middle Eastern desert. When they enter the dig site, which is a large underground laboratory, they encounter a priest who has strange boils all over his body. The team's medic, Doc (Taryn Manning), sedates the priest. Click (Brandon Fobbs) uses the dig sites terminal to activate the elevator and notices something code-named the Gehenna Project, and asks Cardell if she knows what it is. However she denies knowing about it. Mack orders Nickels (Zack Ward) to stay and watch the priest while the rest of the team take the elevator deep into the dig site.
When they exit the elevator they encounter a scientist named Duncan (Bill Moseley) who has strange boils like the priest. Duncan attacks Hammer (Franky G) but is shot in the chest by Mack. While treating Duncan's wound, Doc has a hallucination of her sister being angry at her for letting her die. Duncan and Doc disappear but the team uses Doc's tracking device to follow after them.
The team splits up and Yoshi (Stephanie Jacobsen) follows a hallucination of her and Hicks's (Jason London) unborn daughter. The team runs into Duncan who is trying to open the door to the safe room. Duncan yells at the team about their ignorance to salvation and Mack shoots him in the head, which strangely doesn't kill him, but the entire team shooting him he finally dies. The door to the safety room is opened from the inside revealing a priest named Fulton (Henry Rollins), who tells them that Doc was likely taken to the temple and he agrees to take them there. The team notices that Yoshi is missing and when they find her, she tells the team of her hallucination and Fulton explains that the possessed use visions to tempt humans, Mack then duct tapes Fulton's mouth shut.
Nickels hallucinates a nude woman and he is attacked by the priest. He fights back with a knife but has his arm broken and the priest spits a dark fluid in his mouth, then drags him away. Click is separated from the team and encounters Doc locked in some room and when he tries to help her he is attacked by a possessed scientist but is rescued when Mack and Hammer throw explosives in the corridor where the scientist is which causes the passage to collapse. Fulton and the team arrive at the temple where they learn from Fulton and Cardell that the scientists are possessed because they absorbed the spirit of a Nephilim, which is frozen in the temple, to prevent it from escaping. Fulton explains that the dig site is one of many tombs created by God to imprison Nephilims.
Yoshi follows the hallucination to Doc, who is possessed, kisses Yoshi then cuts her back open. When the team notices that Yoshi is missing, Hicks and Hammer try to find her. When they find her, Doc attacks Hammer and he aims his gun at her after he notices that she has developed boils. Hicks points his gun at Hammer and Hammer tries to tell Hicks that Doc is possessed. Hicks doesn't believe him and shoots at Hammer who manages to run away.
Hicks then chases Doc and then finds Yoshi, whose spine is exposed, he tries to help her but she attacks him and then Doc rips his throat out. Hammer arrives back at the temple to tell Mack about Doc and Hicks. Fulton realizes that Cardell activated the Gehenna Project (which is a self destruct device for the dig site, and runs for the elevator alone) with Click's unintentional help. The soldiers only have fifteen minutes to get to the elevator before the explosion.
The door to the temple slowly starts closing. Mack, Cardell, and Click make it out of the temple but Hammer gets locked in the temple and is surrounded by possessed scientists. He puts up a fight but is overwhelmed and sets off his grenades killing himself and the possessed scientists attacking him. Fulton is pushed into barbed wire by Doc who then slits his throat. Mack, Cardell, and Click arrive at the area where they encountered Duncan for the first time, and they meet up with Wesley who is possessed but doesn't have the boils. Doc and Nickel's, who is now possessed, arrives and Mack and Click shoot him and a few other possessed until the possessed priest grabs Click and drags him away and kills him. Mack has a hallucination of his old best friend Blakely (Ray Winstone) who Mack was ordered to murder years ago. Mack resists and shoots an explosive barrel next to Wesley which burns him and kills Doc and the hallucination of Blakely.
Cardell stands over Wesley and sets his soul free, when Mack tells her that they have to leave she refuses saying that her goal was to set her father's soul free. Mack makes it to the elevator alone and escapes the dig site seconds before the explosion. Mack is then picked up by the helicopter and realizes that he has a new purpose in the world, that hes a new soldier in a very old war..