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Saya wasn't leading the chiropternas. She was supposed to be slaying them. And she was..sort of... but just killing humans and chiropterans indiscriminatly. Saya was used by Red shield as a chiropteran slayer. This is explained in the movie. The Saya in the film was very pissy and slightly angry/angsty/depressed. A combination of these emotions may have been responsible for turning her into what we saw at the beginning of episode 1. Remember, David does say they were trying to give Saya time to awaken on her own because they witnessed the result of forcing her to act.
Maybe you would enjoy watching the movie. There is a graphic novel as well as a series of books based Blood the Last Vampire as well. The first book was recently published. I read it and it does explain Saya's origins to some extent but we cannot be certain the tv series will follow the books. As for the film, the tv series picks up 30 years after the ending of the movie.
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