The movie begins in black and white with Mary Rollins (Shirley McQueen) hiding away her two children, teenage daughter Lindsay (Tatiana Maslany) and young boy Michael (Jodelle Ferland) in an old farm house. She tells her son to be a big boy as they enter a bedroom. All this has been in black and white. The door is closed and begins to shake, the mother puts the boy under the bed. He is crying and she tries to hush him up. The door bangs open and an invisible force throws her against the wall. The mysterious shadow leaves, the boy runs into the hall to his sister. She is just as scared and she asks 'Where's mom?' The force throws her over the banister of the stairs, later she is dragged into the basement by her feet, leaving deep nail marks in the floor. The boy runs into the kitchen and hides in a cupboard. However, the thing comes and after a heart stopping moment pulls him out. The screen fades to black.
Title credits roll. Now the screen is colour and we see a car driving down the highway. They talk and come into the farm we saw at the beginning. Jess (Kristen Stewart) gets out of the car and goes into the house alone. She looks around and behind her the cupboard opens and closes behind her. She looks in and sees a little wind up tractor way back at the back. She reaches in trying to reach it and it lurches forward and begins to move. She is going back out and hears a noise from the basement and the door is locked when she tries it. She notices some strange marks on the wooden floor (the marks which Lindsay had scratched off). Jess goes upstairs and her dad Roy (Dylan McDermott) talks to her about how much she likes the house.
Denise (Penelope Ann Miller) is Jess' mother and sees a watermark on the walls and starts scrubbing it. Later she is flipping the sheets and making waves and the little boy Ben (Evan and Theodore Turner) sees two bloody legs under the sheets. Jess and mom share an odd moment and Jess goes to the basement to put boxes down there when she hears a noise.
A drifter called John Burwell (John Corbett) happens to pass by and is hired to work the sunflower fields. Dad will pay him later when the harvest is sold.
Jess is continually drawn to the cellar with unsettling results. She sees a childlike ghost figure that leaves her with bruises on her arm landing her in the ER. Her parents have left her alone at home babysitting her brother, and she phones the police terrified because they are being attacked and the house is crumbling down. The policeofficer (Michael Daingerfield) says they will let things be only this once, but that if she ever again phones the police saying that there is a lot of damage and nothing has happened, there will be consequences.
The doctor (Anna Hagan) asks the parents if she's had any personal issues that would cause her to want to hurt herself. Mom explains she's struggled a bit with "emotional issues" from the Chicago they left behind. On the car ride home she explains "these things attacked me" but dad wants none of it saying she did it to herself. Jess goes into the house to see a pocket watch open by itself to show a woman's photo inside. Mom and Dad argue about the move to the country and ensuing problems, especially because Roy rejected an offer to buy the farm to some other unkown person with a 15% extra over the price they paid for it, without even telling her. The realty seller Colby Price (William B. Davis) seems weird, but he doesn't seem to have anything to do with the farm mystery afterwards.
Jess takes off on her bicycle and meets up with a boy from town. They ride together into town in his pickup and they discuss how she thinks the Rollins didn't just "leave" the town for good, they died. She shares the story of her drunk driving accident that caused little Ben to be hospitalized. Ben hasn't spoken since. The treatment of Ben's condition has added to the financial pressures of the family, but to no avail.
Back at the farm mom is having chat with Ben. He points outside toward the barn and she asks "what did you see?" He points again at the barn and she asks what he sees and he makes an ugly face pulling down is eyes with his fingers. The crows come back in flocks and begin to attack drifter John out in the sunflower fields. He is beaten by the crows but survives. Denise puts Ben to bed and hears a creaking sound. The stain in the wall is lifesize now as a body appears in 3-D form.
In town Jess goes to the local drug store with her friend Bobby (Dustin Milligan) to watch again the newspaper cutouts. Jess sees a photo of the Rollins family. The man in the photo is the drifter John.
Back at the farm, John remembers his bad harvest; has a flashback of himself overwon by the situation, and the bank manager flashing a deed. He heads to the house as Denise is readying to leave the house with Ben. John flashes back to his own wife and child who were about to leave him and he thinks Denise is his wife Mary. She escapes from him hiding behind a locked door. Jess and her friend arrive back from town and call for mom and Ben while walking through the house with an axe. They are chased through the house by John with walls getting marked up along the way. Jess goes down to the cellar and finds Denise and Ben. They all have seen something. John calls for Mary threatening her with a pitchfork demanding that she opens the door.
John continues his search through the house for his "family" while Denise, Jess and Ben hide in the cellar. Dad arrives back home and asks Bobby where they are. Upon seeing Jess, Roy takes it in the back with John's pitchfork. John knocks Jess about in the cellar. Random objects begin moving toward a spot on the floor and then disappear into a hole. Jess narrowly avoids the pitchfork. She pushes away drifter John and he falls into a now liquified pit, pulled down by the aparitions of the murdered former family. They swallow up John into the pitch-black mud. When John is killed, they think it's over. The pit inhabitants aren't done yet as they reach for Jess. She is saved by Roy and Denise. The police come to investigate and Roy is taken to the hospital seriously injured but alive nonetheless.
Some time afterwards Jess is smiling. The future has Ben speaking, the crops growing and everyone seems happy!
However several crows fly around the farm in a flock...