First Create two menu. one for initial stage and second for after visited PopupActivity.
Replace Your onCreateOptionsMenu() with
@Override
public boolean onCreateOptionsMenu(Menu menu)
{
MenuInflater inflater = getMenuInflater();
if (initState)
inflater.inflate(R.menu.invisible_main_menu, menu);
else
inflater.inflate(R.menu.visible_main_menu, menu);
return true;
}