One way I thought of using is Powerpoint, with clicking hyperlinked action leads to a slide with its event, etc. But before I do so, is there any other free programs that may help with this?
Thank you in advance

If you're only doing a few levels of interactivity you could just use multiple levels of headings in your document and generate a TOC, it would be structured and linked like a little tree. You can use hyperlinks in most/all Office products, but sometimes it's a little buggy. Otherwise, not sure! Good luck!
Lastly, have you ever written a storyline for a game start to finish? If not, start with a linear storyline and familiarize yourself with writing interactive fiction. THEN move on to the confusing, obnoxiously complex behemoth that is branching storylines and non-linear narrative.
Now onto writing the story itself. Start with an outline. Starting by writing the story itself is the equivalent of trying to build a house without any architectural designs. The outline at first should incorporate only the MAJOR branching story trees. Include NO side quests or anything of the sort. Stay broad and high concept. once that is done, rewrite it. Then rewrite it again. Finally when that outline is GREAT, add in additional branching storylines, quests, etc, working your way down and repeating the process. What I mean is first you write major secondary quests into the outline, rewrite, and then make sure that is all working well. Then you add tertiary quests, etc, etc, etc, etc.
Both when outlining and writing the rough edition of your story, I recommend using a flow chart or a mind map. If you go the mind map route (my preferred method for outlining non-linear narratives), Freemind is a great open-source program for creating mind maps. You can find it here: http://freemind.sour...x.php/Main_Page
-- Tom Sloper -- sloperama.com