Programmatically add items to the menu - not hook_menu
I solved this by just appending my links to the menu tree with hook_preprocess_menu_tree

&lt;?php

function my_module_preprocess_menu_tree(&amp;$vars) {

  if($vars['theme_hook_original'] != 'menu_tree__primary') {
    return;
  }

  $node = menu_get_object();

  //Check to see if this is a group node or group content and return the group_node
  $group_node = my_module_check_for_group_node($node);

  if($group_node) {

    global $user;

    $vars['tree'] = str_replace('last leaf', 'leaf', $vars['tree']);

    $result = db_query('SELECT menu_name FROM og_menu WHERE gid = :nid ORDER By weight', array(':nid' =&gt; $group_node-&gt;nid));

    $menus = $result-&gt;fetchAll();

    foreach($menus as $menu) {
      $tree = menu_tree($menu-&gt;menu_name);

      if(!empty($tree)) {
        // render the organic group menu as HTML
        $tree = drupal_render($tree);

        $tree = str_replace('menu nav', 'dropdown-menu', $tree);

        $menu_array = menu_load($menu-&gt;menu_name);

        //format &lt;li&gt; and top-level &lt;a&gt; for bootstrap
        $li = '&lt;li class="expanded dropdown"&gt;&lt;a href="#" class="dropdown-toggle" data-toggle="dropdown"&gt;'.$menu_array['title'].'&lt;span class="caret"&gt;&lt;/span&gt;&lt;/a&gt;'.$tree.'&lt;/li&gt;';

        $vars['tree'] .= $li;
      }
    }

    $vars['tree'] .= $li; 
 }
 ?&gt;