It's a reference to fishing. Catching a fish is fun. Cleaning a fish is unpleasant, dirty work. Imagine catching a fish and handing it to someone and saying "Please clean and cook this fish." They are likely to say "You catch it, you clean it." That means that the job of cleaning is the fisherman's responsibility. "You catch it, you clean it" is an idiom. It means that if something is your idea, and it goes wrong, it is your responsibility to deal with the results. I can't give you a specific answer without more context, but it might mean that "his buddy" has caught a criminal, and the commander is saying "it's your responsibility to interrogate the criminal, write up the report, and do all the paperwork. I won't assign those jobs to anybody else."