Will Byers disappeared as a direct consequence of an experiment which took place at Hawkins National Laboratory. In the experiment, a monster from another dimension entered Hawkins, Indiana, taking Will back to its home dimension.
The laboratory sought to cover up the truth and prevent further investigation into the mystery. They planted the fake body in the local quarry and instructed state trooper David O'Bannon to find it. The coroners who carried on the autopsy were also hired by the laboratory, replacing the morgue's usual coroner.
After a confrontation with David O'Bannon, Chief Jim Hopper suspected that the body was fake. He later broke into the morgue, cutting open the body with a knife. He discovered cotton stuffing inside, proving his suspicions.
Behind the Scenes
Will's fake body looked so realistic that the Duffer Brothers used it again in season 2, in one of the final scenes of the season. In the scene when Joyce, Jonathan and Nancy are trying to rid of the Mind Flayer from Will, there's a part where Nancy has to burn Will with a hot iron to stop him from choking his mother Joyce. The Duffers brought in the fake body for Nancy to burn instead, so no actors got injured in real life.