A Vast improvement from Part One, but...
First let me get the good. The animation are amazing and the graphics show continued improvement. The sound isn't bad, and is well composed. The direction of the action and the pacing of this story is done nicely, and there's an attempt to throw a little humor into a serious movie such as this. I also like how this chapter can be taken stand-alone. While watching Part I is helpful, it isn't absolutely necessary.
But there are two problems with the overall writing that make such a wonderful fall short of excellence.
The first problem is the set of cliches in this piece. I don't expect something without any reliance on the storytelling standards, but you have shown the ability to deliver great material even while relying on the tropes. Then, with Red Riding Hood you didn't just create a "dark" story. You subverted close every trope (both traditional and modern) and along with the direction, acting, and composition, created a masterpiece.
Now with this, you have the standard, "Guy with mysterious object finds supernatural naked woman and must protect her from shadowy bad guys." Given the opening sequence of part one and the spark of power shown in this one, it's likely she's not going to be powerless and naked forever (and from Ken's opening monologue in Part I, this series may conclude on a bittersweet note where he DOESN'T end up with the girl, after all), but my problem isn't that Ken is doing all the work. Rather, every development appears to be derivate to the point where I could not get lost in the telling of the story. The only thing that surprised me even in the slightest is the bullets were able to disintegrate the bad guys.
My biggest problem with this, though, is that your main protagonist, Ken, for all his visual glory, is completely uninteresting to me. I mean, other than his voice there is very little in terms of personality that sets him apart. He has unresolved "daddy issues" and a cop. The problem is this type of hero has been done to death, and is even worse when despite all the character establishment in the first part, there's nothing that really defines this guy other than his childhood trauma.
This isn't bad by any means. But so far, this has been the same old story of shadowy bad guys after a girl and a jewel and a "normal" guy who gets involved. and soon finds his destiny intertwined on the side of good. You've done better and you can do better with a story. I'd hate to let the wonderful package you've put this tale in go to waste.