When Sam and Dean are woken from their sleep by the cellphone ringing, neither expect it to be John Winchester, their dad, whom they haven't seen or heard from in months. He apologizes to Sam for not being there when Jessica died and tells the boys that he needs them to go to Indiana to track down some missing people. With barely another word, he hangs up, leaving them as frustrated as they had been since the start.
Sam doesn't want to go to Indiana. He saw the phone number the call came from and knows his dad is in Sacramento. Dean insists that they need to follow the instructions, and the two argue. Eventually, Sam gets out of the car and starts walking towards the bus station. Dean drives to Indiana and starts asking questions about the most recent missing couple. On the main highway, Sam meets a young girl also hitching a ride. She won't tell him her name or where she's headed in case he's "some kind of freak." She gets in a truck and heads away from him.
Meanwhile, Dean finds out that the couple were in town a year ago and that they headed out via the apple orchard. He follows the directions and as soon as he gets near the orchard his EMF reader starts bleeping wildly. Getting out to investigate, he sees a creepy looking scarecrow in the middle of the orchard. Looking more closely, he realizes that this is one of the missing men. He heads back to town and starts trying to ask more questions of Emily, a young girl who lives with her aunt and uncle.
Back at the bus station, Sam meets the same girl again that he saw earlier. They finally introduce themselves - her name is Meg and she's also heading to California. He ends up telling her a little about his family - how he feels that Dean is always telling him what to do, never letting him choose his own life. Meg sympathizes and the two become friends.
Dean discovers another couple in Burkitsville who he suspects are about to become the next victims. When his attempts to convince them to change their plans fail, he follows them that night. When they breakdown by the orchard, he follows them in. Sure enough, the scarecrow comes to life and heads towards them. Dean shoots at it, distracting it long enough for the three of them to escape. When he turns back, the scarecrow is gone. Next morning, he phones Sam (or Sam phones him!) and they discuss what he's found out. They suspect the scarecrow is being animated by some kind of pagan god, who, once given a sacrifice, keeps the town's crops healthy and the people safe. He hangs up after saying goodbye and goes off to talk to a professor at the local community college. The professor confirms his theories, but as he is walking out, Dean is hit on the head by the sheriff, knocking him out. The sheriff and some of the locals are talking and decide that they still have to find a sacrifice for the scarecrow. Dean rescued the couple that should have been sacrificed, so it was only right that he take their place. In the absence of a girl, they decide that Emily, the niece of two of the locals involved, will have to do.
Dean and Emily are tied up in the orchard ready to become sacrifices, but Sam, who has realized that his place is alongside Dean, arrives and unties them. When they make it out of the orchard, the scarecrow goes after any human sacrifices it can find - Emily's aunt and uncle. With the scarecrow placated for a while, they attack the tree and the scarecrow with fire, burning them down and hopefully ending the cycle for good. Emily, orphaned once again, gets on a bus to Boston, hoping to find a new life by herself. Dean and Sam take a few moments to reassure themselves that their friendship is back where it should be, and then get in the car and head off.
Meg, the girl Sam met at the bus station, is hitching a lift in a van. She tells the driver she needs to make a call and, when he pulls over, she slits his throat with a silver knife, gathering his blood in a bowl. She seems to be speaking to someone through the blood and says she could have stopped Sam. She listens and responds with "Yes, father."