Excellent Job
A very refined game, strong artwork, an actually decent plot (Rare for a flash game), a good upgrading system, responsive and easy controls, side quests, a good selection of weapons each with their ups and downs, and a lot of replayability, courtesy of the mission ranking and level up system.
The enemies do not have much variety but I see no harm in that because the game is too fast paced to have any regards to what kind of odd attack patterns an enemy may have.
The music is decent, nothing too memorable but it is very fitting for the game/story and is of good enough quality as to not be annoying to the player.
The only reason I do not give this game a 10 (Which it is very deserving of in almost every respect) is because the game is far too easy. The enemies do so little damage that there is barely any harm in getting hit by a large multitude of shots in the lightest armor possible, and to make it even easier there are health powerups (Which I never bothered using because I barely took any damage anyways). Keep note that this also makes virtually every health/armor upgrade seem rather useless.
One suggestion would be to upgrade the enemy difficulty as the player levels up, this way difficulty with balancing the leveling system along with the mission system is no longer much of an issue and the game is kept challenging at the same time.
Overall, an excellent game with an obvious lot of work put into it, and is very easy to get immersed into. I look forward to seeing your next game, this is executed in a manner of excellence very rarely found among flash games.