Neon Genesis Evangelion - Gakuen Datenroku Manga

Shinji Ikari spends his days at the NERV Foundation Academy (A catholic school) in a peaceful yet bored stupor, when one night, after witnessing the figures of Rei Ayanami, the object of his affection, and a boy he’s never seen before running from the scene of a violent explosion, he happens to find an odd gem. Soon after, he meets the transfer student Kaworu Nagisa, the fleeing boy he’d seen with Ayanami, and is forcibly recruited to assist Rei, Kaworu, and Asuka Soryuu Langely in fighting the “Angels”, beings who wish to destroy the Earth, because of the “Core” he collected that night.