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<!doctype html>
<html lang="pt">
    <head>
        <meta charset="utf-8" />
        <meta name="viewport" content="width=device-width, initial-scale=1.0" />
        <title><?=$page_title?></title>
        <link rel="shortcut icon" href="<?=site_url('favicon2.ico')?>" type="image/x-icon">
        <link rel="icon" href="<?=site_url('favicon2.ico')?>" type="image/x-icon">
        <link rel="stylesheet" href="<?=site_url('/css/bootstrap.min.css')?>">
    </head>
    <body>

<footer class="footer">
            <script src="<?=site_url('js/jquery.min.js')?>"></script>
            <script src="<?=site_url('js/bootstrap.min.js')?>"></script>
            <script src="<?=site_url('js/jquery.mask.min.js')?>"></script>
            <script>
            <!-- Por exemplo um script só para uma view em específico -->
            <?=$page_script?>
            </script>
        </footer>
    </body>
</html>

<?php require_once(dirname(__FILE__).'/header.php'); ?>
meu conteúdo da view usuário...
<?php require_once(dirname(__FILE__).'/footer.php'); ?>

public function minha_url() {
    // ...

    $this->load->view('header', $data);
    $this->load->view('usuario', $data);
    $this->load->view('footer', $data);
}