The story running along with this is great. I definitely like how you've pit the corporation versus the ethics of the church and continued further to corrupt them.
I hope in the next flash that the motives of the corporate side are shown. Although in the beginning it explains what they've done, but only a vague overshadow. It still kind of leaves you floating there on why the church dislikes them. But this had a wonderful mix of hilarity and action. I noticed on the molotov scene that the guy with the yin-yang eyepatch had ":3" on his shirt.
Also, the detail through the sequences was tremendous. I have to say my favorite part would be in the fight scene when the camera zooms in to the teeth of the one that flies towards it. And you seemed to keep your characters well proportioned through it too.
I can't really tell you much to improve on that hasn't already been touched on with you, but it was a great flash.