You asked about a fic you had read and posted this in a blog a few months ago- "Please ask about this fic. I do not know title or author's name, but I know the plot. Someone will recognise Maybe it and help to find it. Illya is dealing with a unit which infiltrated THRUSH KGB. He works undercover, everybody thinks he's a Soviet spy, only Waverly knows the truth. Napoleon is unaware of what's happening, but he refuses to take Illya as an enemy and tries to help him. It seems to me there was an episode in which the partners met for the first time and started working together. A gen's It fic"
In LJ, we have a "Fic Find" site where friends help us find stories like the one you asked about. Here is the response from one of the members. She believes the story you were looking for is called "Disheveled" by Lyrebird. Be advised, however, it is slash or at least pre-slash. I haven't read the entire fic.
web.archive.org/web/20081012060323/http://lyreb...