themes/default/theme_file.php:

<?php
$header = <<<EOH
<script ...>....</script>
EOH;
include('header.php');
?>
template stuff, html in the middle.
<?php include('footer.php'); ?>

themes/default/header.php:

<html>
<head>
....
<?php
if(isset($header)) echo $header; ?>
</head>
<body>
Navigation...