This article proposes a new three-stage stochastic framework for dealing with predictable two-phase natural disasters in distribution systems. This framework is a multiobjective optimization, in which the amount of curtailed energy, the number of switching actions, and the vulnerability of operational components are selected as the main criteria for decision-making process. The optimization problem is formulated in the form of a stochastic mixed-integer linear programming (MILP) problem. In this article, a windstorm event followed by flooding is analyzed as a two-phase natural disaster. In this regard, the uncertainties associated with gust-wind speed, floodwater depths, and load demands are taken into account by the proposed framework. The initial configurations of islands are formed just ahead of the storm event (first stage), and their borders are changed in the second stage, which is associated with the storm event and its aftermath. The final configurations of islands are determined by the third stage once the uncertainties of floodwater depths are revealed. In the proposed framework, the emergency generators (EGs) are assumed to be prone to flooding, and a novel approach is proposed for quantifying the flood-related failure probability of EGs. Likewise, overhead distribution structures are recognized as vulnerable components to storms. The proposed framework is implemented on a test system, and its effectiveness is investigated and verified through seven case studies.