The four parts are The Beginning, The Big Three, The End, and Side Quests. Shadowrun is technically a linear game, meaning that each time you play, you go through the same steps and get to the same ending. However, the order in which you go through each of those steps is up to you. It's like the Mega Man series, where you can pick the order in which you fight the stages, but you always end up at Dr. Wily's fortress. So, do the Beginning, work on each of the Big Three however you choose, do a side quest or two if you feel like it, then do the End. Simple, right? On with the walkthroughs...