Brilliant
IMO, this is the best top-down space shooter since Raiden or Drakojan skies. When I read "pre-rendered Graphics and rich storyline", I got a little worried, as many flash games possess those, but still have crap gameplay. However, you managed to make a game with both original gameplay(for a flash game of this genre), and beautiful graphics.
On a side note, I liked Raiden's music better, as it felt a bit more riveting. Whereas Drakojan's gameplay felt a bit more harrowing and kept me on edge. I would also like to be able to switch ships between levels. On the second Level, I felt a bit robbed when the boss killed me in one hit(I had full health!).
Regardless, this is the best shooter to grace newgrounds in quite a few months, I hope you get voted game of the year.