title_body: NCX TOC - Hide the external TOC in EPUB 2?
upvoted_answer: You cannot deactivate/remove the ncx file. As the epub will not validate without it. Why dont you just simply remove all the links from within it, that way, if a reader does open it up in a sidebar it will simply show a blank screen. Not really user friendly though. I would recommend you add atleast one entry, pointing to the start of your book or your "internal toc".
  Taking the above into consideration your navmap inside your ncx file would look something like this:
  
  &lt;navMap&gt;
      &lt;navPoint id="navpoint1" playOrder="1"&gt;
          &lt;navLabel&gt;
              &lt;text&gt;Your book title&lt;/text&gt;
          &lt;/navLabel&gt;
          &lt;content src="page1.xhtml" /&gt;
      &lt;/navPoint&gt;
  &lt;/navMap&gt;