Computer security has been plagued by increasing formidable, dynamic, hard-to-detect, hard-to-predict, and hard-to-characterize hacking techniques. Such techniques are very often deployed in self-propagating worms capable of automatically infecting vulnerable computer systems and then building large bot networks, which are then used to launch coordinated attacks on designated targets. In this work, we investigate novel applications of Natural Language Processing (NLP) methods to detect and correlate botnet behaviors through the analysis of honeypot data. In our approach we take observed behaviors in shell commands issued by intruders during captured internet sessions and reduce them to collections of stochastic processes that are, in turn, processed with machine learning techniques to build classifiers and predictors. Our technique results in a new ability to cluster botnet source IP address even in the face of their desire to obfuscate their penetration attempts through rapid or random permutation techniques.