This is one of the most difficult parts of the Internal Assessment to unpack because they are integrated. In other subjects, the scope and method are very separate; in history less so. One colleague likes to tell her students that the scope is the what and the method is the how. I agree to a certain extent, but feel that can cause some confusion.
The scope of an investigation would be the parameters. If you choose to write your IA on which Doctor was most important to the global appeal of Dr. Who, then this would include the doctors you choose to examine.
The methods are the approach that will be used to answer the RQ. Here you would have the issues you are going to explore to determine global appeal of Dr. Who: personality, story line, quality of writers, etc.
You may want to tell the reader about how you are going to conduct the research and, strictly speaking, you are correct. However, that is not what the IB is asking for. It is assumed that you will be conducting research either online, at school or at a library, and then will develop a plan. You do not have to include the sources you will use in section C, but if you are doing historiography and if those are the main sources, it might be appropriate – if not exhaustive.
All in all, the Plan of Investigation is short – most teachers recommend 150-200 words – so choose your words well!