The Qwaser of Stigmata/WMG

Hardcore Christians only pretend to hate science, but they actually invented chemistry.
All Christians (at least those of the Eastern Orthodox sect) seem to have surprisingly good knowledge over atomic structure, the way they can manipulate it to power themselves or de-power others, like using oxygen to instantly rust metal or mixing chlorine with hydrogen in water to create instant acid. Considering Joshua's power, they even foresaw that at least 111 elements would be discovered.

Jesus was the first Qwaser.
Considering he was able to turn water into wine, loaves into fishes, and more, he must have had quite a bit of knowledge of how to manipulate objects at the atomic level, like many Qwasers do these days. You know what this means? Jesus was the first chemist ever, and Mary was probably his teacher...or at least his Soma donor.
 * Funnily enough, the end of the manga reveals that he was a Qwaser (can't remember if he was the first one, though) and his element was iron.

The Nazis aren't dead...
...they were simply lying in wait (for 60-70 years) for the time when a couple of Japanese schoolgirls would lead them to the reincarnation of Mary. Just As Planned!

Lizzy's real Identity is actually this universe's Saber
Or at least she's a Gender Bender, time-warped version of King Arthur. Yeah obvious WMG is Obvious, but someone had to write it.

Katja is a Timelord
Her previous incarnation was the Alexandra and her TARDIS is her robotic puppet Anastasia