You fundamentally misunderstand MVC, at least as implemented in CI.
All URLs of your site (at least those that use the CI infrastructure) are displayed in functions (methods) inside the controllers.
http://myCIsite.com/controller/method[/var1†[/var2] ...
It doesn't matter if the URL is accessible via plain HTTP or through AJAX. It is always a one-to-one mapping. Because of this, you should think of the controller / method combination as a "web page". Do not think about presentation as a web page.
Models and views are subordinate to controllers. The controller delegates certain responsibilities to them - interacting with databases for models and displaying the page in views.
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