What drives the main menu?
You can see region--menu.tpl.php which is rendering main menu..

&lt;div&lt;?php print $attributes; ?&gt;&gt;   &lt;div&lt;?php print $content_attributes; ?&gt;&gt;
    &lt;?php if ($main_menu || $secondary_menu): ?&gt;
    &lt;nav class="navigation"&gt;
      &lt;div class="primary-menu inline"&gt;
        &lt;?php print theme('links__system_main_menu', array('prefix' =&gt; '&lt;div&gt;', 'links' =&gt; $main_menu, 'attributes' =&gt; array('id' =&gt; 'main-menu', 'class' =&gt; array('links', 'inline', 'clearfix', 'main-menu')), 'heading' =&gt; array('text' =&gt; t('Main menu'),'level' =&gt; 'h2','class' =&gt; array('element-invisible')))); ?&gt;
      &lt;/div&gt;
      &lt;div class="second-menu inline"&gt;
        &lt;?php print theme('links__system_secondary_menu', array('links' =&gt; $secondary_menu, 'attributes' =&gt; array('id' =&gt; 'secondary-menu', 'class' =&gt; array('links', 'inline', 'clearfix', 'secondary-menu')), 'heading' =&gt; array('text' =&gt; t('Secondary menu'),'level' =&gt; 'h2','class' =&gt; array('element-invisible')))); ?&gt;
      &lt;/div&gt;
    &lt;/nav&gt;
    &lt;?php endif; ?&gt;
    &lt;?php print $content; ?&gt;   &lt;/div&gt; &lt;/div&gt;