Net‐Centric Operations (NCO) is operated on a System‐of‐Systems (SoS) communication environment. Emergent behavior is one of the five SoS characteristics. Layered SoS architectures start from the top SoS‐level containing emergent behavior. Conceptual agent‐based modeling was presented to simulate the four principles of emergence. The simulations covered the condition of emergence, non‐linear behavior and coupling relationship between agents. The four principles are interrelated. The emergent behavior has impacts on traditional systems engineering process. Neural network artificial intelligence may be needed to assist the understanding of emergent behaviors for architectural model development. Agent‐based modeling needs further development and should be integrated with neural network and SysML.