Something that comes up in Cop/crime TV shows at times is the villian who is impossible to take down legally because they are an informant for some federal agency such as the FBI. It might be an interesting twist if they found out that the big bad villian is being protected by her own agency, the FBI, say because they are a very important informant on some corp or syndicate.
That's just... epic. =)
To be more specific: I had already planned on doing SOMETHING in which "the shadows are the only recourse" for your plucky FBI agent, but to have the villain untouchable because they're protected by the FBI itself... huh. Wow.
