Generally your js files will have objects and Methods that are called/used from you main page. So you html wiil look like :
<html>
<head>
<title>Title of Document</title>
<script src="path/to/file/fileName.js"></script>
</head>
<body onload="showAlert();">
The content of
your page goes here.
</body>
</html>
and you js will look like:
function showAlert(){
alert("This is an alert box");
}