You could try loading your content (html, js) through the phonegap inappbrowser plugin and seeing if that would work.
You might run into issues with cross domain security.
The other solution would be to create API services on your server and have the html & js in the phonegap app consume the server side services.
We have a very thorough API on the server...
So I guess in the phonegap app... we just call to the api...