The Great Cataclysm & Amaterasu: The series reveals that the Great Cataclysm 250 years ago was an attempt by the Evangelist to merge Earth with Adolla. The survivor, Amaterasu, was not a goddess but a human girl with an Adolla Burst, who was shoved into a generator to power Tokyo, living in constant agony.
The Holy Sol Temple: The religion was founded by Raffles I, but it is revealed that Raffles was killed and replaced by a shape-shifting agent of the Evangelist, meaning the entire faith was designed to gather Pillars for the next Cataclysm.
Shinra's Lineage: Shinra and Sho are "Pillars" needed for the apocalypse. Their mother didn't just die; she became a powerful Demon Infernal who has been watching over them from Adolla.
The Ending (Connection to Soul Eater): In the final arc, the Cataclysm occurs, but Shinra evolves into 'Shinrabanshō-man' (a god-like form). He absorbs the collective consciousness of humanity and rewrites reality. He creates a new world where the concept of death is less absolute (death becomes 'violent' or cartoony rather than final tragedy), creates the first Shinigami (Lord Death), and effectively births the world of Soul Eater. The series ends with Shinra depowering himself to live as a normal boy in this new, 'mad' world.