Each of these would have a substantive part of your argument, but it wouldn't read in a linear fashion. Then you could also have a document that contained the key passages that you wanted to analyze. Each passage could have some explanation beneath it about the role in the book, but there would be other links in the text as well. Throughout the paper he has built in hypertext links across his own argument to show the interrelatedness of his ideas. The key to the ability of the reader to navigate this hypertext is the use of both internal and external links.
Internal links are the links that target a link to the same page.
A second example of writing a nontraditional paper that plays with form and format would be this. This is a really a variation of the above without the annotated passages. In this case, you would write your sections on key ideas as a series of short documents. There might be an overview page, then a series of four or five other pages. See below for examples of this kind.