If you simply use the standard, unmodified fe_page template, everything should work perfectly. It sounds like you removed (or never added) this line just before the closing <body> tag: <?php echo $this->mootools; ?>
The following code is rendered by this tag, which you should find at the end of your page source once you correct the template.
Code:
<script type="text/javascript" src="plugins/mediabox/js/mediabox.js?1.2.0"></script>
<script type="text/javascript">
<![CDATA[//><!--
Mediabox.scanPage = function() {
var links = $$("a").filter(function(el) {
return el.rel && el.rel.test(/^lightbox/i);
});
$$(links).mediabox({/* Put custom options here */}, null, function(el) {
var rel0 = this.rel.replace(/[[]|]/gi," ");
var relsize = rel0.split(" ");
return (this == el) || ((this.rel.length > 8) && el.rel.match(relsize[1]));
});
};
window.addEvent("domready", Mediabox.scanPage);
//--><!]]>
</script>
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