1> The puppet kid is a spy for Angel, isn't he? In an early episode, Shura commented about not being the only spy Angel had sent to True Cross. We don't know what or who he really is, though. I like to imagine that he's the archangel Uriel who's working with the Vatican.
2> Not sure. They had a key, but I don't understand how that would help them from inside a ball of foliage.
I assumed that Egin (the grandfather) had resurrected the Polish teacher's wife. Egin was willing to use tools that others would consider immoral (as in, the bomb to destroy the holy world and those hideously cursed weapons that were passed out to the exorcists), and he would have had time to find the artificial life facility.
3> Satan is an immortal. Maybe he could be obliterated, but destroying the gate that he was possessing wouldn't destroy him. And he didn't really give up; he was defeated.
4> Mephisto's Ultimate Goal: Making sure that life isn't easy for anyone?
This show is a B+ for me. It's not perfect, but it is fun, contains fascinating characters, is beautifully drawn as a whole, and bravely incorporates religious and literature references that (I assume) are completely unknown by most of its primary target audience and are rarely considered by its expanded audiences.
I can forgive that important aspects of the show are left to the imagination, because that's typical in Japanese animation. Anyway, the movie might explain more.
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