According to Scott McCloud, one of the distinguishing features of comics as a medium is that it substitutes space for time. Past and future are always visibly available around the point that the reader is paying attention to, and sophisticated writers can take advantage of this. And yet, nearly all experiments in interactive comics -- including McCloud's own -- take it for granted that interactivity negates this, and that making a choice in the story means that the story past the choice point isn't available to the reader yet. Interactivity is, after all, something that takes place in actual time, not in the space of the comics page.
Alternately, you have things like Jason Shiga's "Meanwhile" that are interactive in the same way as Choose-Your-Own-Adventure books: they show a simultaneous branching of paths, but you can't actually change the state of the thing. In this case, interactivity, like narrative time, is a property of what's printed on the page.
Unfortunately, I never came up with a story to take advantage of this, so all we have is this prototype, which illustrates that the system is capable of nesting branches.
See also First Draft of the Revolution by Emily Short and Liza Daly for a vaguely similar experiment.