Or, ‘what I learned from dnd and storytelling for a group’
1. Create the big bad final horribleness and the encounter that goes with it. Be as absolutely rediculous as you want, because chances are this will be the final thing any of your PCs get to do in your campaign. If they get to do anything else in your campaign it should be related to Epic Destinies and the conclusions thereof.
2. Create some enemies of roughly 5 levels lower in difficulty than the final badness, these are the string pullers and campaign shakers of the story you are telling. Figure out what each one of these enemies is out for, do they serve their own agendas, or work for others?
3. Figure out based on these lower levelled foes, what kinds of forces they are likely to control. Who does the bidding of these figures of darkness and what drives them to do so?
4. Change things up a little by making some of the foes allies for the PCs, how much can the PCs trust them if the foe made friend has their own agendas?
5. Rewind time until the badguys and friends and foes and even the PCs are only just starting to awake to the power inherrent within. How do the badguys go about becoming those huge monsters you originally created? Do the PCs meet any of them early on and get to know them over the course of the adventure path? Foreshadow the growing threat against the PCs by throwing them into the course of events and having them shift and change the direction of your game now that you know what everybodies motivations are.