In conventional agriculture, pests and pathogens are managed with pesticides to minimize crop loss. However, studies have shown that such practice may lead to pest resurgence, often associated with the elimination of natural enemies. Because similar phenomena in plant-pathosystems are rarely discussed, our study investigates whether pathogen resurgence can occur. We compare two natural enemies in the plant-pathosystem: a typical predator, which consumes the pathogen immediately, and a hyperparasite, which infects pathogens but allows them to survive for a period, resulting in a stage structure of the pathogen population. To explore this, we constructed models with different natural enemies in a host-pathogen system, and we increased the intrinsic mortality rate of the pathogen to simulate pesticide application. When the natural enemy is a predator, an increase in the intrinsic mortality rate of the pathogen does not alter the equilibrium abundance of the pathogen until the predator is eliminated. However, in the system with a hyperparasite, the Hydra effect occurs: the equilibrium abundance of the pathogen paradoxically increases with an increased pathogen intrinsic mortality rate. This is because the high pathogen intrinsic mortality rate reduces the hyperparasite abundance, weakening the top-down effect and allowing more pathogens to grow, even under a high intrinsic mortality rate. Our finding suggest that the pathogen resurgence stems from the Hydra effect induced by the hyperparasitism. We further explore how the Hydra effect affects the system with two pathogen strains, characterized by a virulence-to-host and susceptibility-to-hyperparasite trade-off, and find that the Hydra effect can help the virulent strain outcompete the mild strains. From the results, it is evident that field management strategies should not solely focus on eliminating target pathogens, as this may overlook the existing top-down effect of hyperparasites on pathogens and thus prove counterproductive. Overall, this research highlights the importance of considering potential species interactions when developing management strategies in the field.