It was serialized in Shueisha's seinen manga magazine Weekly Young Jump from January 2012 to March 2016.

Ten years ago, Ryōta Murakami along with his childhood friend, Kuroneko set out to search for signs of alien life.

Since then, he has been continuously staring at the night sky in order to prove that aliens exist, and also to fulfill Kuroneko's dying wish.

Ryōta becomes a part of Neko's life, learning more about her dilemma and the hidden forces that exist in the universe.

The institute meaning "witch castle" is the Organization that unearthed aliens in Germany by gold miners and a Japanese geologist (Ryouta's great-grandfather) in 1910, but never made it a public discovery, instead began the top-secret research over it to sought God's destruction.

A resistance group meaning "witch hunt" that is built by scientists who defected from the Organization due to the threat that they posed to God himself.

Written and illustrated by Lynn Okamoto, Brynhildr in the Darkness was serialized in Shueisha's seinen manga magazine Weekly Young Jump from January 26, 2012, to March 31, 2016.