The story of your game shouldn't be too linear... Not a Point A goes to Point B to Point C to Point D. The player should be able to make some decisions and not strictly guided on every aspect, otherwise you may not have replay. An example would be if the player needed to get to the coastal city of Lahspe, and had three routes to take: (1) By boat, (2) on foot and (3) by caravan. Each will eventually lead to their destination, but you may encounter new characters along one path, new weapons at another and it could have an effect on final chapter of your game.
Still, your main goal would likely remain unchanged. Perhaps subtle changes added into the ending depending upon the player's actions. Sure, you took the boat to Lahspe. You meet Boo. She's joined your party. The arch villain recognizes her as the girl she left alive. Uhhh ohhhhh... However, that might just add a nuance not expected.
Some sites on flowcharts if you're interested:
Creately
Create Flowcharts Online
Or you can add side-quests into the game. Harkening back to Final Fantasy, Yuffie and Vincent were very popular characters that only join your party if you succeed in finding them and completing their sidequest missions. However, sidequests could also be entertaining if only to add flavor to cities and towns. You may rescue a dog that fell down a well (dangit... it belongs to the kid that pick pocketed me the moment I arrived!), or you may defend the honor of some bar maid from a half goblin that made some racist slur. These do not need to affect your game.
In difference to my friend JayRay, I would keep my material within a folder on my desktop and keep the work offline to prevent theft. Separate documents for characters, stories, folders for the graphics and acquired subject material, the game concepts and backups of the game itself. KEEP BACKUPS!!!!!
The reason I say offline is that I am aware of theft of game material. One of my friends was working upon a game and she asked another friend to craft a unique battlesystem. Even though the battlesystem was kept within a locked forum, the custom battlesystem was stolen and subsequently published among other boards. Unfortunately, the battlesystem and its specialized gameplay was a key factor in her game and its release to the public took away the novelty of her game.
So... anything special... offline.
OH! Moved into 'Upcoming Projects' BTW. You had it in our Forum Games board.