A project to save humankind, developed under secrecy by the former Fenrir Far East Branch Director Schicksal. It was a bold project under which a man-made Apocalypse would be triggered after evacuating some humans away from the planet to serve as "Seeds". Using Aegis as a hideout, he had been nurturing Nova to trigger the Devouring Apocalypse, as well as to maintain control over the planet's environment after the apocalypse. The Former Director also needed to obtain Shio's core to awaken Nova.
The Far East Branch director, Johannes von Schicksal, was put in charge of developing the Aegis Project, a project whose ultimate purpose was to create an Aragami-impervious utopia for mankind to live in. At some stage during the development of said project, he realized that such utopia would sooner or later be attacked by Aragami and humankind would be once again defenseless against them. With that revelation, he put the Aegis project on hold an began the Ark project, in which he would trigger a controlled apocalypse to rid the world of all Aragami and create a permanently safe haven for the remaining humans or "Seeds" that would be away from the planet during the apocalypse. To do that, he needed to nurture a huge Aragami that could trigger said apocalypse, Nova, and he needed to obtain a special Aragami's core, the Singularity. He began nurturing Nova by sending high-rank God Eaters on "Special missions" which usually implicated retrieving an Aragami's core (meaning they were nothing more than missions to "gather food" for Nova), and put his son Soma Schicksal to search for the Singularity.
During the development of the project, Lindow Amamiya was commanded by a higher authority to investigate on the Ark project and inform about the Director's secret plan. The latter elaborated a complex plan to get him out of his way, utilizing Dr. Daigo Oguruma to brainwash the recent transfer Alisa Illinichina Amiela and force her to kill Lindow during the Moon in the Welkin mission. While he did not kill Lindow, he did succeed in getting rid of him by making him an MIA (Missing In Action) God Eater.
In the meantime, Dr. Paylor Sakaki managed to send von Schicksal in a hunt after the Singularity, which was supposedly in Europe, while he could find and hide the real singularity with the aid of the 1st Unit.
Later on, Sakuya Tachibana became aware of the Ark project thanks to some data Lindow had left behind, and decided to investigate the matters on her own, despite the fact that the rest of the 1st Unit was aware of the project. Despite having stated that she wanted to infiltrate Aegis on her own, Alisa managed to follow her and disable most of the defense systems in Aegis. The director, who was present at the moment, tried to use Alisa's mental instability to his favor once again with the aid of Oguruma, but Sakuya and Alisa managed to go fugitive nevertheless.
The director then went public with his project, causing mixed reactions among everyone in the branch, ranging from initial acceptation from Kota Fujiki to clear opposition from his own son, Soma. Eventually, he discovered that Sakaki was hiding the actual singularity from him, and took Shio away with him to Aegis, which had transformed into Nova's hideout by then.
The entire first Unit, including Kota, managed to enter Aegis and tried to stop the director from achieving his objectives. While they defeated him after he became part Aragami, they couldn't stop Nova from devouring the world, an event that was luckily avoided by the fact that Shio managed to retain her consciousness after becoming Nova's mind, and drove Nova to the moon to save the Earth.