You can do it:
include(dirname(__FILE__)."/init.php");
$GLOBALS['ISC_CLASS_ORDER'] = GetClass('ISC_ORDER');
$GLOBALS['ISC_CLASS_ORDER']->HandlePage();
echo '<script type="text/javascript">YOUR JS HERE</script>';
OR
<?php
include(dirname(__FILE__)."/init.php");
$GLOBALS['ISC_CLASS_ORDER'] = GetClass('ISC_ORDER');
$GLOBALS['ISC_CLASS_ORDER']->HandlePage();
?>
<script type="text/javascript">YOUR JS HERE</script>
Hm?
, HandlePage() - , Class ISC_ORDER- > handlePage(), ... ...
EDIT:
<?php
echo '<script type="text/javascript">//<!--
alert("Hello to multiline JS script");
alert("Do You get it?");
//--></script>';
?>