I see you are trying to load a website as a mobile app - you may review this article. Please note that Apple App Store may reject your app if it only opens a web page inside an app.
As to your question - to load the content in the WebView:
- without using the inAppBrowser plugin - set the allow-navigation tag in your iOS config file so that the WebView itself can be allowed navigation to a specific site without opening Safari
- when using inAppBrowser - open the link by setting the target to "_self" which would open the URL in the Cordova WebView
Still, event with the above method you would loose the access to Cordova Native APIs. In general in a Hybrid app you have a starting/main index.html and when you navigate to different views, the same index.html gets different DOM elements added/hidden and thus different views are shown/removed. Thus a Hybrid app is similar to a single-page application - you navigate through the different DOM elements of that page and not through different pages.
All app logic is saved in window.app object of the loaded index.html. When loading the page, cordova.js is loading the Cordova Native APIs in the window object as well. Therefore, when you navigate to a different .html page all data and methods are lost (window object is overwritten as well as all methods and data saved, as if the application is closed).
I hope this has helped.