Graham Hess (MEL GIBSON) is a single father who's raising his kids, Morgan (RORY CULKIN) and Bo (ABIGAIL BRESLIN), on their Bucks County, PA farm. A former reverend, Graham has given up religion due to the untimely death of his wife, Colleen (PATRICIA KALEMBER), some six months ago in an incident that involved local veterinarian Ray Reddy (M. NIGHT SHYAMALAN).
Local police officer Caroline Paski (CHERRY JONES) tries to help out, while Graham's younger adult brother, Merrill (JOAQUIN PHOENIX), has moved in to do the same. That all changes, however, when large and unexplained crop circles suddenly show up in the family's cornfield.
Their fascination with them turns into horror when they see TV footage that not only shows similar circles appearing around the world, but also indicate what looks like the beginning of an invasion by extraterrestrial visitors. As things progressively worsen, the family finds both their safety and beliefs severely tested.