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I have a popup.html opened when the user clicks the icon. The popup.html has a button. If this button is clicked i want to show another popup from a different html file after closing the current popup. Does anyone know how to do this.( I already have a listner attached to my button. All i want to know is hot to close the currently displaying popup and open a new one).

Popups are like regular tabs so window.location.href="..." works on them.
But you can simply popup an overlay and a fullscreen iframe inside the popup window and overlay a close button over that one.
<iframe src="http://target.com" style="position:absolute; left:0; top:0; right:0; bottom:0; width:...
So on.

You can use innerHTML to update popup page dynamically
var event_container;
event_container = document.getElementById('element ID');//Get location of event container
event_container.innerHTML = event_container.innerHTML + "html string you want to add";