This paper proposes a new kind of cyber-security system, named Botnet Defense System (BDS), which defends an Internet of Things (IoT) system against malicious botnets. The concept of BDS is “Fight fire with fire”. The distinguishing feature is that it uses white-hat botnets to fight malicious botnets. A BDS consists of four components: Monitor, Strategy Planner, Launcher, and Command and Control (C&C) server. The Monitor component watches over a target IoT system. If the component detects a malicious botnet, the Strategy Planner component makes a strategy against the botnet. Based on the planned strategy, the Launcher component sends white-hat worms into the IoT system and constructs a white-hat botnet. The C&C server component commands and controls the white-hat botnet to exterminate the malicious botnet. Strategy studies are essential to produce intended results. We proposed three basic strategies to launch white-hat worms: All-Out, Few-Elite, and Environment-Adaptive. We evaluated BDS and the proposed strategies through the simulation of agent-oriented Petri net model representing the battle between Mirai botnets and the white-hat botnets. This result shows that the Environment-Adaptive strategy is the best and reduced the number of needed white-hat worms to 38.5% almost without changing the extermination rate for Mirai bots.