Around A. D. 1400 (600 years ago), there must have been a crisis for the Village Farmers. At that time, the number of Native American communities, and probably numbers of humans in the villages, dwindled. The territory that would become Nebraska was almost deserted for hundreds of years.

Nearly a century before Columbus' landing, Central Plains Tradition villages were abandoned. Communities that once covered most of present-day Kansas and Nebraska plus portions of Iowa, Colorado and Wyoming moved or died. For the next 300 years, communities were confined to the Missouri River and its tributaries in extreme northeastern Nebraska and a few large villages along the Missouri in South Dakota. The plains of Nebraska were virtually unoccupied from A. D. 1400 until the Pawnees, Omaha, and Otos — tribes that European explorers came to know in historic times — came back into the region in the 17th and 18th centuries. For those 300 years, archaeologists lose the trail of the Central Plains Tradition culture.

Archaeologists continue to search for clues to the mystery of what happened to the prehistoric Village Farmers. Nebraska was not the only region to experience major cultural change in the 100 to 200 years prior to European contact. Complex societies, such as the Anasazi of the Southwest and Mississippians of the Midwest and Southeast, all began to crumble after 1300 A. D. What caused such widespread change at that time might include a major change in the climate, overpopulation, inter-tribal warfare (over food, timber, and animals), or disease. For example, the onset of a "Little Ice Age" around 1300 A. D. may have caused environmental deterioration and helped force native inhabitants of Nebraska to move elsewhere.

What had been a successful adaptation to the environment by the Central Plains Tradition village farmers apparently failed.

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