I am calling the javascript window.open() function to load another url in a pop up. Once the users is finished it takes them to the last page that has a link that says close
The answers as they are require you to add code to the spawned window. That is unnecessary coupling.
// In parent window
var pop = open(url);
pop.onunload = function() {
// Run your code, the popup window is unloading
// Beware though, this will also fire if the user navigates to a different
// page within thepopup. If you need to support that, you will have to play around
// with pop.closed and setTimeouts
}