When Israel had finished killing all the men ¹  of Ai who had chased them toward the desert ²  (they all fell by the sword), ³  all Israel returned to Ai and put the sword to it.

Joshua and the Israelites almost totally wiped them out, but some survivors did escape to the fortified cities. ¹ 

Indeed, for forty years the Israelites traveled through the desert until all the men old enough to fight when they left Egypt, the ones who had disobeyed the Lord, died off. ¹  For the Lord had sworn a solemn oath to them that he would not let them see the land he had sworn on oath to give them, ²  a land rich in ³  milk and honey.