In a cooperative scenario after you have a concept of NPCs, you should think where and when can the PCs meet them. These places and times should be the scenes in the scenario.
In a competitive scenario you can choose the arena at your taste where the PCs will fight, and then think about what NPCs will they meet there.
In either case you should draw a diagram wich shows the players wich scenes can be entered from wich scenes via travel or elapse of time. It is a good idea to make a circle to give the PCs more chance in the same scene repeating all over. You can alternate scenes wich are uneven: in one the PCs have the opportunity to attack an NPC and exact secrets, in the other the NPC is mighty enough to have revenge if the players haven't won the scenario yet.
A circle can be a day (work at the office, lunch in the cafeteria, business meeting at evining) or a week (weekend with the family and children after work). But if you are doing circles of scenes don't forget to define a "time" limit or it will continue endlessly.
The most important of a scene is to define how strong the NPCs become by changing their tactics. Side effect is that their secrets can change, too.