I am glad that you have kept up with the good flashwork, there is real improvement to be tracked in your submissions!
I usually start off with the storyline, and this will be no exception. Your story is extremely comprehensive. I like that you have a distinct setting, with politics, factions, maps and a history. Its probably way too much story for the average newgrounder, but its cool that the option to read about it is there. On that note, I would have made the text a bit larger, and perhaps another font like Calibri. Sometimes its a bit hard on the eyes(; The story in the animation itself is not the easiest to follow, but its still good stuff. In the start though, it was hard to follow what the radio said because I was also reading the computer screen.
The graphics have improved greatly, but there are some mixed styles in here. Some places (like the computer screen) are very detailed and with very good use of gradients. Other places the graphics look just fine, but if you used gradients in a similar fashion there (like on the characters) the result would be perfect(; Especially in the 3d scenes I would have liked to see a bit more detail.
The animation is quiet good. Some places it is very well coordinated, other places you could have made them smoother and not as fast. Especially the movement of hands where unnaturally fast at some times. Once again I like how you move the scene for a cinematic effect, although you did not use this very much in the start. Are you using V-Cam? V-cam is a very good tool for cinematic effects.
The audio is very good, I like how detailed it is; theres a sound for almost everything:D The voice acting is also very good, but the quality of the audio is a bit lacking there; but it did not really bug me much(;
Basically, this is an outstanding product, I can feel all the hours and hours (and hours) of work that you have put into this. I give you 9 of 10 because there are some stuff in here that I know you could have done better, but really, its good sh*t!