As with jQuery, you can use .load to dynamically load a file.
I'm using using a pretty large script that uses Prototype JS framework, so I can't implement jQuery because they conflict. (I know of the noConflict workaround however this script is so big I can't implement that into every file).
Does Prototype have a similar function to dynamically load another file?
It sounds like you are describing XHR which in Prototype is conveniently presented as Ajax.Updater
.