i remember only one of the first episodes. There is a little girl who is either lost or running from something in the woods when she stumbles into a really big building that turns out to be a school, but it's no ordinary school. One of the teachers thinks that the girl is a transfer/new student that they were expecting, but never showed up, and bring her inside where she finds out the school creates a (I don't wanna say robot but like a robot) living thing from dead things and makes them fight. I also remember there is a graveyard episode where they have to dig up something and make it into one of their creations.
It is also in, I think, a more "realistic" anime art style.