Around 9,000 years ago, humans had mastered farming to the point where food was plentiful, and began moving into large settlements. Abruptly, these proto-cities were abandoned - one of the greatest mysteries of early human civilisation.
     Agriculture emerged about 12,000 years ago, during the Neolithic. Nomadic groups began settling in small villages for part of the year, soon began living in villages for whole seasons, and finally settled down for good.
     Some of those villages, like Catalhoyuk in central Turkey, grew to a few thousand people, with thousands living there continuously from about 7500 BCE to 5700 BCE. Catalhoyuk had none of the features we associate with the grand, walled cities that emerged thousands of years later in Africa, Asia and the Middle East. There were no palaces, no massive ziggurats or pyramids dedicated to the gods, no signs of class distinction. Every family had a small one-room home with a hearth. Each home was roughly the same size. Streets didn't exist. Homes were erected next to each other. People walked over roofs and went through doors in their ceilings. There was art, but no writing, and little in the way of specialised labour. Unlike ancient Uruk or Mohenjo-Daro, there were no cottage industries. Families lived mostly by keeping farms and small herds of animals in the nearby hills.
     Settled life wasn't easy. Dependent on a few local food sources, humans become vulnerable in ways that hunter-gatherers never were.
     In the mid-5000s BCE, Catalhoyuk was suddenly abandoned. The same thing happened to several other outsized village-cities in the Levant. People returned to small village life for thousands of years, and we see a similar pattern elsewhere in the world: intensification of farming, booming population, growing settlements, abandonment.
     Catalhoyuk was once surrounded by gushing rivers. In the late Neolithic, the weather cooled down and dried out. Catalhoyuk could no longer sustain itself on locally-grown crops. Scattering into smaller villages gave people a settled life without depending on massive crop yields.
     University of Notre Dame anthropologist Ian Kuijt describes the expansion and abandonment of a mega-village called Basta, in what is now Jordan. The people of Basta invented two-story architecture, and began sub-dividing their living spaces into smaller and smaller rooms, many with specialised areas for living and for food storage.
     Kuijt believes people abandoned Basta because its population outstripped its belief systems. The people in Neolithic mega-villages inherited a system of social organisation from their nomadic forebears. Nomadic life requires everyone in the group to share resources to survive - a very flat social structure, as reflected in the built environment of Catalhoyuk.
     This works nicely in a small community, where you know all of your neighbours. With a thousand people, it's harder to have a flat social structure. Some people start to do specialised tasks, and social differentiation begins. Agriculture gave humans the means to grow into large settlements, but Kuijt hypothesises that they weren't ready to abandon ancient practices, preferring to abandon their cities when times were tough. When cities re-emerge in the 4,000s BCE, they have rigid social hierarchies, and systems of writing to tally up who lives where and owns what.

Edited from io9 (17 November 2014)