The Internet has a constantly growing number of users. With this increase, also comes entities that wish to exploit this group in malicious ways. Botnets are one of the malicious methods and it can be viewed as an enabler for illicit commercial activity. The Botnet owner controls hundreds, thousands or even millions of victim computers and harnesses their combines computing power to do illegal actions. Some examples are spam mail trafficking or distributed denial of service attacks among other illegal acts.To reduce the threat posed by botnets, this thesis focuses on the research of the newest type of the botnets which are Peer-to-Peer based. Our case study examines Storm worm, one of the most prolific botnets in the world. Our research is based on how to disrupt botnet communications and we provide an approach to increase the effectiveness of botnet countermeasures. The primary contributions are: (1) We define a mathematical model for the Storm worm which can also be applied elsewhere. (2) We first provide an algorithm to find strategic high traffic communication points. Masquerading as these strategic points is advantageous for mitigating the storm worm. To validate our algorithm, we simulate a storm worm environment and use strategic nodes to impede the storm worm communication.