Climate change, pandemics, and economic crises have created complex challenges for supply chains. Managing such situations requires the development of reliable decision-making frameworks. In this paper, a multi-level, multi-product, and multi-period closed-loop supply chain is studied with environmental considerations. A bi-objective mixed-integer linear programming model is presented for facility location, flow allocation, and transportation mode determination. The objectives of the model are to minimize the total cost and maximize the reliability of suppliers to meet the needs of factories. In the area of reliability engineering, a new approach is defined for modeling the probability of supplier availability considering catastrophic failures caused by pandemics, economic sanctions, and other failure modes. Furthermore, the decision-maker can handle the emission of greenhouse gases by an upper-bound constraint. In order to face the simultaneous uncertainty of demand and the maximum CO2 emission allowed, a scenario-based two-stage stochastic programming approach is proposed. The improved version of the augmented ε-constraint method, known as AUGMECON2, is used to solve the proposed model. The efficiency of the model and the proposed solution approach are investigated through a real-world case study of a battery manufacturing company in Iran.