This paper proposes a novel energy management system (EMS) for an isolated structure of networked microgrids (NMGs). The interconnected microgrids consist of the cyber-physical connections for information and power exchanges. A bi-level EMS is presented in which the outer-level EMS is aimed to exchange the required information and power between the interconnected microgrids, and the inner-level EMS is intended for energy scheduling of each on-fault microgrid in case of separation from other microgrids. This paper focuses on the operation of interconnected microgrids. A step-wise demand response program (DRP) is also considered in the energy management to attain the cost-effective operation. Furthermore, a new pricing model based on microgrid marginal pricing (MGMP) is introduced for the power exchanges between the interconnected microgrids. To cope with the uncertainties of the renewable energy sources and loads, some scenarios are generated using the scenario-based analysis. Also, a backward scenario reduction method is used to reduce the number of the scenarios. Besides, a mixed integer linear programming (MILP) is applied to the stochastic optimization problem of the NMGs. The proposed model is implemented on a test system with five NMGs. The simulation is run over a 24-hour scheduling time horizon. Both cases without and with demand response program (DRP) are compared in the numerical results. The results of the simulation demonstrate that using the proposed DRP in the energy management increases the performance of the generation units and decreases the total operational cost of the proposed NMGs. Also, the voltages of the buses converge to their rated values.