I'm using the Yoko theme. I tried switching themes but the result is always the same. I have pasted 404.template from the Yoko theme below. But I never get to see Yoko's 404 page, all 404's directly jump to the home page. I have disabled all 404 related plug-ins.
The current behavior (404 jumps automatically to home page) is not bad. But it would be nice to get control over it again.
I did establish that my .htaccess was destroyed by activating the "404 Redirected" plug-in. This plug-in replaces .htaccess with a blank file and does not restore it when deactivated.
This is the Yoko theme's 404 template (which I never see so I don't think it is the problem):
* @package WordPress
* @subpackage Yoko
<h1 class="entry-title"><?php _e( 'Not Found', 'yoko' ); ?></h1>
</header><!-- end page-entry-header -->
<p><?php _e( 'Apologies, but the page you requested could not be found. Perhaps searching will help.', 'yoko' ); ?></p>
<?php get_search_form(); ?>
// focus on search field after it has loaded
document.getElementById('s') && document.getElementById('s').focus();
</div><!-- end content -->
<?php get_sidebar(); ?>
<?php get_footer(); ?>