The Messengers opens with a family being killed in a farmhouse, one by one. The last one is a small boy hiding in a cabinet with a toy. He is yanked out by what is assumed to be the killer and then the film cuts to a new family on their way to the farmhouse they have just purchased. Looking for a new start away from the city, a family of four have purchased the farm to start a sunflower farm. The oldest daughter, Jess was involved in an accident where she was driving drunk with her toddler brother in the car. He was seriously injured, but recovers. He has not spoken since the accident, and the parents have a difficult time trusting their daughter.
As the family settles into their new home, crows seem to come from everywhere and are continuously swarming over the farm. The father, Roy, is attacked by crows who are chased off by a stranger who appears looking for work. Meanwhile, the little boy, Ben, is seeing ghosts of the family members that had been killed in the home, and his sister senses something, but can't see them until she is dragged toward the cellar by one while babysitting. She calls the police who find nothing and her parent do not believe her, thinking she wants to leave and go back to the city.
Jess is later attacked in the barn, suffering cuts and bruises that her parents believe to be self inflicted to get what she wants. She is determined to prove to her parents she is not doing it herself, so does some research in town about the house. It seems the family that lived there. She is told they disappeared six years earlier, and when she sees a photo of the family she realizes that the man her father hired to help around the farm, John, was the father of the missing family.
During this time, Denise, her mother, is putting Ben down to sleep when she sees the stain on the wall she had cleaned reappear. The spirit of a woman comes out of the stain frightening her badly. She then packs the family's bags and puts them on the porch while waiting for her husband to come home. John becomes confused and thinks she is his wife trying to leave like before. Denise gets Ben and hides in the cellar after locking the door. Jess arrives, and gets into the cellar with her mother and helps her barricade it further. As John breaks in, Roy arrives to help and is stabbed by John with a pitchfork.
At this point, the spirits of John's murdered family come up out of the ground of the cellar and drag him down with them. He tries to grab Jess' leg to save himself but her parents fight him off. After the paramedics arrive, Roy and Denise apologize to Jess for doubting her, and the film ends with the family living on the greatly improved looking farm, with Ben talking and all seeming to be happy.