Most scientific articles are written as if the research followed some kind of waterfall model. In other words, a typical paper proceeds pretty linearly from the idea to the results to the implications of the research, hiding the fact that one thing might have lead to another in a very non-linear way.
I guess the reason for the linear format is to attempt to make the research easy to digest for others, and to keep the paper as short as possible. However, what should one do when following the standard format becomes a too large burden (e.g. excessive cross-referencing), or hides a key insight about the research process itself, which could be valuable for others to know?
Though most of the papers publish only mention their liner approach, some do try to mention the multiple path summery (mostly psychological research), but that's where citing comes, an author conducts his/her research in a single path with controlled conditions, and opens door to other authors to take other path.
Even if you plan to include all the possibilities of your research outcomes, you should first follow waterfall model, and just jot down other possible outcomes for future, because reaching the destination is initially lots of trial and error process.
PS: it will mostly depend on your area of research and the approach you are taking