Medium Voltage Direct Current (MVDC) power distribution architectures are of immense interest for various shipboard power applications due to their advantages over classical MVAC distribution systems with respect to power quality, power density, and efficiency. However, MVDC are far away from maturity when compared to MVAC with respect to fault detection and isolation. Currently, there are no standards available for applying MVDC protection systems in shipboard applications. Furthermore, due to the absence of zero crossings in DC waveforms and unique transient fault signatures, it is challenging to design effective protection system schemes to isolate faults via conventional protection systems. This paper investigates and analyses various types of shipboard MVDC dynamic fault behaviours and signatures under different DC bus disturbances such as: bus to ground, bus to bus to ground, and impact of Pulsed-Power Load (PPL) with and without faults on a shipboard MVDC distribution system. Furthermore, a communication-based fault detection and isolation system controller that improves upon a directional ac overcurrent relay protection system is proposed offering additional protection discrimination between faults and PPLs in MVDC systems. To validate the effectiveness of the proposed protection controller, different bus current disturbances are simulated within a time-domain electromagnetic transient simulation of a shipboard power system including a PPL system operating with different ramp rate profiles, pulse widths, peak powers, and fault locations