The first thing is the combo-system, which is the big point awarder in both Story and Extra Mode. How does it work? Is it about how many fairies you can pop without actually shooting the ones after the one up front?
The combo system pretty much works like this: Destroy a fairy or activated spirit, small blue ring explosion, chain reaction causing fairies and spirits to cause similar small blue explosions, everything that can disappear is added to the combo counter (spirits, fairies, and pellet bullets). Of course a combo stops itself if you start another one during the first combo.
I think that's pretty much it.