Jennifer Pailey (Joanna Going) is bringing her younger sister, Lisa Pailey (Rose McGowan), home with her for a visit, to the little town of Snowfield, Colorado, where she is the M.D. She's been concerned for her sister's welfare, living in Los Angeles with their alcoholic mother, getting involved with shady characters. Snowfield, a former mining town turned tourist destination, offers fresh air, quiet, fewer hoodlums to associate with, and hopefully, an opportunity for Lisa to sort out what she wants to do with her life.The town is very quiet indeed on this late fall afternoon. It's the off-season for tourists, but they also see none of the 400 year-round residents. They drive up to Jenny's residence/office, hoping that Hilda, Jenny's housekeeper (Judith Drake), has made good on her promise of apple pie for dinner. Instead, they find her dead in the kitchen, a terrible look of fear on her face, every inch of visible skin bruised and blackened. The phone is also dead...and creaking noises upstairs suggest an intruder may still be present, so they decide to go quickly to the deputy sheriff's office.Oddly, Jenny's Jeep won't start. Neither, it seems, will any other vehicle in town. Nightfall is coming on, so they hurry to the deputy's office on foot. Deputy Henderson (Larry Odien) is also dead, the condition of his body like Hilda's. But there is a further mystery here... he had drawn his gun and fired multiple rounds. As a professional law enforcement officer, presumeably he would hit what he was shooting at...yet there is no sign of another body or a blood trail. Jenny gets a shotgun from the deputy's gun rack, loads it (with help from Lisa) and they head for the bakery. If they're likely to find anyone, Jenny tells Lisa, it will be there: the owners, Jacob and Anna, also live in the rooms above the bakery and they're always there. The front door is locked. They hear sounds and see shadows that indicate they are being followed. They run down the alley and go in through the back door. They are greeted by the grisly sight of two severed hands lying on a workbench, still grasping a rolling pin. The timer on the oven starts to buzz loudly... Jenny opens it warily: there are only some cake layers baking. They are momentarily relieved--until Jacob's and Anna's severed heads fall down onto the cakes!Huddled together, they make their way toward the front of the bakery. Night has fallen and it's very dark. The phone rings... Jenny answers, but there is no human voice on the line, just an eerie, muttering whisper. They turn to leave again...only to be blocked by three men holding flashlights and guns. Deputy Henderson had been on the phone with headquarters when the line went dead. Sheriff Bryce Hammond (Ben Affleck) and two deputies, Steve Shanning (Nicky Katt) and Stu Wargle (Liev Shreiber) have come to investigate.They decide to return to the deputy's office, but as they step outside the bakery, every horn, siren, whistle and bell in Snowfield suddenly goes off... the deafening noise goes on for a full minute. Then, just as suddenly as it began it all stops, and the only lights left on are at the Candleglow Inn up the street. It seems they're expected there next. A glance at the guest book in the lobby shows there are only four guests. Faint music starts to play upstairs: Patsy Cline, singing I Fall To Pieces. Sheriff Bryce and Deputy Stu go up to check the rooms... the women follow at a little distance with Deputy Steve.Sheriff Bryce enters one room and finds it empty... he opens a closet door, and is confronted with a vision (flashback?) of a young boy (Luke Eberl) aiming a gun at him. It disappears almost immediately, but Bryce is very shaken by it. Deputy Stu enters another room and finds the body of a young woman lying on the bed. She has the bruised look of the housekeeper and deputy, but she is also attractive and shapely. Stu sits on the bed next to her. "You wanna tell me what happened here?" he murmurs, and then snickers oddly. He puts a hand on her leg, on the bare skin below the hem of her skirt. At that moment, Sheriff Bryce walks in. "What are you doing, Stu?" he asks. Stu jumps up, startled, embarrassed, at a loss to explain. "Looking for clues?" the sheriff suggests, sarcastically. Stu says yes... but both men know what was going on. Bryce decides to let it go: "Watch the hall, Stu", he says, and leaves. When he's out of sight, Stu laughs again, his strange, wheezing snicker, and with a last glance back at the dead girl, follows Bryce into the hall. "Hey," he says to Lisa, leering down at her, "you wanna see somethin'?" She looks at him with disgust, and says "No," emphatically.Bryce has found the room where the music was playing, on the bedside radio. He switches it off and asks Jenny to come in. He shows her the bathroom: it was locked from inside, he'd had to break in... but no one is there now, and there are no other doors or windows. Someone has written on the mirror in lipstick, "Dr. Timothy Flyte - The Ancient Enemy". He asks Jenny if she's ever heard of Timothy Flyte; she tells him no, he's not a local.From another empty room, they all hear a sound like metal chains being dropped. They enter cautiously and find a large pile of metallic objects lying on top of the bed: jewelry, buttons, watches, gold teeth... and more. "Whoever it is, he strips them to the skin," says Deputy Steve. "Beyond the skin," says Dr. Jenny, in an odd tone. As they all look at her, she picks a flat metallic disk out of the pile. "It's a pacemaker," she tells them.They go back to the lobby to regroup and discuss. They hear the music start upstairs: Patsy Cline again. A woman suddenly screams outside, "Help--Help me!" Deputy Steve shouts, "Cover me, Bryce!" and runs out with his gun drawn. Bryce calls for him to wait, and follows, but it's too late: they hear him scream, and when they get outside all that's left are his empty shoes and his gun spinning on the pavement.They go back to Deputy Henderson's office. They zip Deputy Henderson into a body bag, and take him down to the basement. Bryce tries to radio for help. He tells the deputy on the other end of the transmission about Dr. Timothy Flyte, and asks them to send help from the local military installation, but the transmission is garbled and broken, and finally collapses. They are not sure how much--or if any--of it was heard.Bryce and Stu load as many weapons and lay out as much ammunition as possible, preparing for a siege. The lights go out, they all hear something at the window, and see a huge, almost man-sized moth hovering there. The two men fire at it again and again, until it goes away. After a moment, Stu walks over to look out the ruined window. The creature flies in again, grabs him by the face, slams him against the opposite wall, and flings him down. It flies around the room a few moments longer, threatening to grab each of the remaining three humans in turn, while Bryce shoots at it over and over without effect. At last, it flies out the window.Deputy Wargle is dead... his face and his brain, incredibly, were completely consumed in the few moments the creature had hold of him. They zip him into a body bag of his own, and take him to the basement to keep company with Henderson. Bryce nails a sheet of plywood over the broken window. They settle down to wait for morning...wondering if they'll be allowed to do that.At the editorial offices of Wide World News in New York City, Dr. Timothy Flyte (Peter OToole) is working late. Formerly a distinguished member of the faculty at Oxford University, he has been reduced to writing articles for this sleazy tabloid because the subject of his research was considered fanciful and ridiculous. He is approached by two men (Robert Knepper, Bo Hopkins) from the FBI. They "ask" him to go with them as a matter of national security.In Snowfield, while Lisa is trying to nap in a jail cell, Dr. Jenny and Sheriff Bryce are in the next room talking. It turns out he is a former FBI agent, too, who came to be sheriff in this rural county because of an incident that occurred in a raid on a drug house during his former career. He'd opened a closet door to find a gun pointed at him, had fired on the suspect and killed him, only to find out the suspect was just a child, and the gun was just a toy. He'd been cleared of any blame, but had been unable to overcome his guilt. He still carries a newspaper clipping of the event. The boy's picture is in the article. We see he is the phantom Bryce glimpsed earlier in the closet at the hotel.Lisa interrupts their conversation to ask for an escort to the restroom. Bryce checks inside, finds it clear, and leaves her there alone. She is standing at one of the sinks, getting a cigarette out of her bag, when an odd squealing sound wafts up out of the drain. She almost convinces herself that it's nothing, until a toilet in one of the three empty stalls behind her flushes. She cautiously goes to inspect them, finds nothing--and as she is closing the last door finds Deputy Stu behind it, leering at her. "You wanna see somethin'?" he asks. She runs out screaming. Bryce goes in with gun drawn to investigate, and finds nothing. They check the body bags in the basement: they're both empty. They begin to speculate: could it be moving through the town through the sewers and drains?Dr. Flyte is en route to Snowfield with General Leland Copperfield (Clayton Powell), as part of a large, specialized response team: scientists and military personnel, a couple of large, sophisticated mobile labs, and an armored strike vehicle...prepared to deal with whatever threat they may find. General Copperfield asks Dr. Flyte to tell him about his theory of the Ancient Enemy. Dr. Flyte explains that throughout history there have been incidents of unexplained mass disappearances. He cites the abandoned Mayan cities of Copan, Piedras Negras and Palenque; the "Lost Colony" at Roanoke; the army that vanished outside Nanking, China in 1939. He postulates that an undiscovered entity that exists deep in the earth may be responsible for these incidents...and if not stopped, it could eventually cause the extinction of the human race.They arrive in Snowfield, and Bryce, Jenny and Lisa come out to meet them. "The first thing we need to know," says General Copperfield, "is what kind of threat we're dealing with... chemical, biological, or other." "At the moment," replies Bryce, ruefully, "I'm kind of leaning toward 'other'." The team spreads out and the scientists begin gathering data. They encounter many weird and frightening sights... including another pile of metallic objects in the church, in front of the altar. "Like an offering," says one of the scientists. Dr. Flyte corrects him: "Undigested remains," he says.Over the next few minutes, in a stunning series of horrific events, the whole contingent is wiped out, leaving only Dr. Flyte, Sheriff Bryce, Jenny and Lisa. General Copperfield is last to be killed: a pair of oily black tentacles seeps up through the pavement, penetrates his hazmat suit, and an oily black liquid fills the suit and smothers him. Dead, but still standing, he leans over and smacks the faceplate of his helmet against the pavement, shattering it. He straightens up again, slowly removes a large curved piece of the glass from his mouth, regurgitates into it and puts it on the pavement in front of Dr. Flyte. The eerie voice that was heard on the phone now speaks clearly from his mouth. "My Flesh," It says, and as It does so, the liquid in the glass resolves itself into a small, spotted gecko. "Study it. Write the gospel. But do not try to leave. Witnesses to the Miracle." Message delivered, the general's body topples over, and the oily black substance oozes out of the suit, leaving it collapsed and empty on the pavement.They take shelter in one of the mobile labs. Dr. Flyte begins to analyze the tissue sample. Theorizing, they come to the conclusion that this Entity has lived in the depths of the earth for eons, growing to immense size, and absorbing knowledge from its prey. It can separate off parts of Itself to send as drones, warriors, phantoms... having them assume the shapes of anything or anyone It has absorbed, even of people or monsters from their memories and dreams. With these, It has manipulated Bryce, Jenny and Lisa into bringing Dr. Flyte here... to be Its prophet... to write Its gospel. For It has come to think of Itself as God--or Devil, perhaps because this is what some of Its terrified victims may have thought in their final extremity: Omnipotent... Immortal... Indestructible.Dr. Flyte's analysis reveals that It is closely akin to oil in Its chemical composition. He tells the others that there is a manmade bacterium among the samples in the lab that was developed to break up and disperse oil spills. IF...they can culture enough of it, and IF...they can figure out a way to deliver it, and IF...they can draw the whole mass of It to them long enough to infect It... they MIGHT be able to destroy It. Bryce asks Dr. Flyte if he's sure this will work, and Dr. Flyte says yes...then adds, "Unless there's a nucleus, a small inner mass, that can tear itself away from the core and survive on its own." "You know," says Bryce, wearily, "I really just wanted you to say yes, there."The bacterium is cultured, and loaded into glass vials to be launched by compressed air guns of the type used to shoot tranquilizers into large animals. Dr. Flyte steps outside, walks up to an open manhole and calls to It. He says that he must see It--all of It--in order to be able to write of It. It remains silent, hidden. He says that he knows It has been wondering what they're up to in the mobile lab. He tells It that the others have been preparing a weapon to destroy It. "Even after all they've witnessed tonight," he says, "they still don't believe you're a god. They think you're just a thing, an animal." He waits...still It doesn't appear. His voice turns warm and inviting, as he continues: "What they don't know is that death is for mortals, not for gods. Show yourself... gods have nothing to fear." He waits a few moments longer. Then with just the right taunting note in his voice, he adds, "or DO they???"It appears first as a single person, standing silently on the other side of the manhole, opposite Dr. Flyte... an instant later all 400 residents of the town are standing there before him. Then all the people begin to merge and meld into one swirling mass, which resolves Itself into an immense, hideous, writhing millipede, standing upright. Bryce, Jenny and Lisa run out of the mobile lab, and fire their weapons into the It... "INFECTED!!!" shouts Dr. Flyte, triumphantly. It screams, and begins to flail around violently. Jenny and Lisa run for shelter into the nearby deputy's office, and there, reload their guns. They are pursued by a drone of Deputy Stu. They empty their shotguns into him, knocking him down, blowing away great chunks of his legs and arms. They pause, finally...he is still for a moment, as if dead... then he begins to sing: "I Fall To Pieces". Tentacles shoot out of his arm- and leg-stumps, which he uses to drag himself toward them. They flee up into the ceiling, and he follows...but he is ill, infected by the bacteria, and this makes him more angry and dangerous. "What did you do to me?!?" he bellows at the women. Jenny blows his head off with a shotgun. Incredibly, a hand shoots out of the neck stump and reaches for Lisa. Jenny fires her last vial of the bacteria into the neck stump, and at last he stops...the Deputy Stu drone rapidly dissolves into a revolting liquid.The greater mass of the Entity is also breaking up, like a drop of oil in soapy water. Bryce follows the last of It down into the sewer. He turns a corner, and finds himself face to face with the boy he shot and killed during the drug raid. He hesitates...a tentacle shoots out of the boy's mouth, and knocks him literally for a loop. The air gun is knocked in one direction, and the extra bacteria viles are scattered on the ground in another. Before Bryce can get to them, the boy scoops them up. He balances them in his hand, with an insinuating smile. Bryce draws his handgun. "Always this urge to shoot little boys," says the drone, mockingly. "No," says Bryce, "this time I'm going to miss." He shoots the vials in the drone's hand... they explode, spraying liquid all over him. There is a moment of quiet, then the drone begins to tremble, and then to shake violently... It cannot hold Its shape any longer, It shrieks and groans as It devolves...with one final ear-shattering scream It is gone, and Bryce makes his way back to the others.As a helicopter arrives to rescue them, Dr. Flyte announces to the others that the Entity has won after all: It wanted him to tell the world, and that's just what he's going to do. The scene shifts to a quiet bar, where an old cowboy (Lonnie Chapman, uncredited) and a young cowgirl (Yvette Nipar) are watching Dr. Flyte on the bar's TV. He's wrapping up the narrative of a documentary about the Entity, saying that a watch must be kept for It...for if It wasn't completely destroyed, one day It may destroy mankind."Do you believe that crap?" asks the old cowboy. "I dunno," says the cowgirl, "stranger things have happened. Patty said that Glen was abducted by aliens." The cowboy scoffs: "Glen wasn't abducted by aliens, he run off to Los Angeles... and if you was married to Patty, you'd run off too." A strange, wheezing snicker is heard at the other end of the bar. The other two look in that direction, and the girl asks, "Does that sound funny to you... officer?"Stu Wargle stifles his laughter, and swallows one of the peanuts he's been eating with his beer. "No, ma'am," he says, with mock sincerity... and then he adds slyly, "Hey... you wanna see somethin'?"