Intriguing!
The series keep getting better as the story unfolds! A good quality not seen everyday, certainly here on Newgrounds. You keep the viewer interested from the beginning to the end. The alliance is also a nice new development!
The only criticism I can think of concern the graphics. I presume you use a 3D-modelling program for 'drawing' the vehicles and planes, and some of the men. The fact that you use Flash for drawing the faces and planets and some other objects is really noticable, altough not very disturbing.
My point being, raising the quality of the hand-drawn Flash graphics would really raise the level of the overall graphics.
Other then that you've got a fabulous story here!
Keep it up!