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This paper rigorously shows in the framework of poly-agent systems theory that it is very natural for an innovative society to emerge stratification of networks to cope with complexity intelligent decision makers of it have to deal with. Before introducing poly-agent systems theory, I will first refer to empirical observations of emergence of stratification of networks in innovative societies, which motivate this research. I, then, theoretically show that coexistence of both networks and hierarchies is reasonable and inevitable for a tightly interrelated society because it can provide the decision makers with mediation, which is beneficial for the decision makers as well as the society as a whole. Finally, I will go back again to implications from our theoretical study.