The Tree of Beginnings, or Tree of Genesis, is the source of magic used by the Kusaribe Clan. It manipulates the world's logic. It was suspected to be the murderer of Aika Fuwa, and the tree plots the meeting of Hakaze Kusaribe and Mahiro Fuwa in order to help Hakaze to break the time prison. Samon predicted that it will eventually destroy mankind if it is revived; this was proven to be true as the legends, passed down to the Kusaribe Clan were discovered to be intentional lies. In the series it has began its revival and is now currently fighting with the Tree of Zetsuen. It was shown that the Tree of Beginnings devours civilizations and attempts to dispose of Mahiro and Yoshino Takigawa because the Tree of Beginnings had accomplished its goal by using them to save Hakaze from the time prison.

According to Aika Fuwa, it is impossible to understand what objective the creators of the tree had. In her own theorized words, the creators were possibly "trying to help humans achieve the next stage of evolution or, by defeating the tree, the maturity of the earth will be acknowledged and earth might be allowed to join the supreme galaxy alliance. Or the aliens are possibly betting on how many times earthlings need to defeat the tree."