EXPERT RESPONSE
Be very careful here! While a few botnet specimens are using encrypted peer-to-peer communication technologies, which make them more resistant to monitoring and shutdown attempts, many of today's botnets still rely on a centralized command-and-control structure, often based on Internet Relay Chat (IRC). By sniffing the traffic as an infected machine logs into the botnet, you can watch what the system is up to and potentially see the attacker's commands. Sometimes, an investigator even stumbles upon the user ID and password for controlling -- not just accessing -- the botnet and can then steal the keys to the attacker's castle.
Using that information to interact with the botnet, however, is dangerous. Suppose that you, with the purest of intentions, log into the botnet control channel and issue a command to shut the botnet down or delete the bots. You might inadvertently delete some really important corporate data, or disable a critical server, causing significant financial damage. The large organization that you just affected might turn around and sue you, not the original botnet owner. The attacker might have set up a booby trap so that the botnet goes ballistic if someone else tries to control it. Inadvertently, your actions might cause massive harm.
Beyond that, there is the possibility of retribution. Even if you don't cause damage to the infected machines, there is the not-so-small matter of breaking the bad guy's botnet. The attacker may take this pain out on you by launching a massive flood. One should not trifle with people who manipulate hundreds of thousands of machines and make serious money based on their control.
That said, there is some interesting research being conducted by individuals looking into the actions of large-scale botnets and their operators. I'm not suggesting that such research should be avoided altogether. I am, however, emphasizing that such investigations are not for the faint of heart, must be carried out carefully and could result in some serious negative repercussions. Make sure you consider these issues. For most security people working in most enterprises, such risks aren't worth it.
More information:
Ed Skoudis explains if it's possible to detect peer-to-peer (P2P) botnets.
Learn how attackers can use the Storm worm to strengthen their botnets.
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