I am new to AngularJS and trying to evaluate it for my new web application.
I will have one ASP.NET Web API which will be consumed from an And
I think you are on the right path. I would store the tokens in an Angular Service to make it easier on yourself (http://blog.brunoscopelliti.com/deal-with-users-authentication-in-an-angularjs-web-app). I'm a little confused on what you mean by "AngularJS tries to make a call to ASP.NET MVC application to get HTML", you shouldn't need to secure the MVC app, it's just running your Angular right? The API is the piece you want to secure as well.