Did you know that you may be found responsible for plagiarism even if you don't know what it is? Under this Honor System, it is your responsibility to know. Even if you didn't mean to do it, if you did commit plagiarism, and you get caught, it doesn't matter very much that you didn't know.
Having said that, what if you are sure you didn't plagiarize and the professor says you did. For example, the professor says you must have bought the paper on the Internet because it was so much better than the other stuff you wrote. If you can show him or her your drafts, the notes you took, and any other materials you used in writing the paper, then you probably will be able to show that it was your own work. If you have nothing to show how you wrote it, it's going to be harder to prove. Still, if you can talk convincingly about the material in the paper, including things you decided to leave out, why you made the argument the way you did, how the writings you cited fit into the paper, where you found those writings, etc.--you should be able to convince either the professor or the Honor Council's investigating officer that it was your own work. So keep your notes and learn the material well. Visit the professor's office during the course of working on the assignment to discuss your argument. Engage in an email discussion with him or her. Keep the emails and you'll have more evidence that you did write it. Note that in order to do this, you need to get started early. You won't have much time to engage your professor in conversation if you are first working on the paper at 3 am the night before it is due.