Meh.
Look, this really wasn't that good. The least of your troubles was that this uses every anime cliche in the book and lacks any good characterization, not to mention acts "dark and edgy" without any really good reason behind it.
However, the graphics and animation are just abysmal. 50% of the animation consisted of awkward-looking motion tweens, the other half still looked stiff and awkward. The character drawings themselves were almost hilarious. The faces had almost no structural consistency, and I could swear I saw a few Zelda CD-i-esque faces in there that made me burst out laughing, and not for single frames either. Multiple consecutive frames and stills.
The body proportions had little consistency, either. One moment, the villain's head is huge and his neck is small, and another it's tall and skinny. And I'm almost certain the girl's boobs grew 2 or 3 cup sizes from the beginning to the end.
The voice acting could have been better. I'll just leave it at that.
Anyway, some words to help you consider improving: work on your anatomy a lot more. Do a bunch of life drawings, not just anime. And pick up some animation books, clean up your lines and avoid motion tweens like the plague. They look like garbage.
Also, try to come up with a story that keeps me more interested. I didn't feel any sympathy, hate, or anything for the characters. The girl's betrayal also felt like it came out of nowhere.
They're not interesting, they don't feel like real people to me. Just generic anime characters. You know, robotic dolls that beat each other up, inject each other with mysterious drugs, and act like ninjas.
I simply didn't feel anything when the hero died. In fact, I was laughing my ass off from the downright goofy facial expressions.
Now, I understand that a lot of Newgrounders are going to call this review "useless." Not that I care, but keep in mind, a review that tells the author what needs to be fixed is going to help him a hell of a lot more than a bunch of perfect 10 reviews with nothing to say.
And to the author, before you jump to conclusions, I don't hate you or anything. I just want to see improvement, and hopefully not complacency. I'd like to see you succeed, but you need to do a lot of work before I'll go and call you "professional." So take it easy, alright?