This paper proposes a decentralized control algorithm for the medium-voltage direct current (MVDC) shipboard storage system to enhance the onboard survivability. The algorithm takes decisions based on local measurements, which makes it robust against cyber-attacks and able to provide a fast response. The voltage profile of the MVDC bus has sufficient information about the system status, which is utilized for managing the hybrid energy storage systems. Insertion/removal of the storage devices, such as batteries and supercapacitors, is made according to the mathematical morphology-based voltage processing and state-machine logic algorithms. To ensure proper power sharing, an adaptive droop control is used, taking into account consideration the state-of-charge of the storage units. Field-programmable gate array in the loop validation results confirms the ability of the proposed controller to maintain the MVDC bus voltage and the adequate operation of the storage entities simultaneously.