The best way to make something utilising the Story Zone is to use FPSC itself. Basically, you can set up a scene (make a new level), and add the characters that are going to partake in it. Then, using scripts and waypoints, you can basically direct your characters to move how you wish.
Now that the scene is set, you can use a program like
Fraps to record the scenes and then import them into something like Windows Movie Maker, order them and make the necessary adjustments, and then export it (making sure you export it as an .avi). WMM would work quite well in your case, since it's free, and it has effects (like one for Aging Film, if your "history" goes back that far).
There's a sticky on this board (
here) which also gives a good tutorial on making cutscenes--you just need to scroll down a bit.
Evil has a new name. Demo out now!