The root is of course the World Tree, Yggdrasil, who receded back into the earth when given the task of holding the entity known as Lilith, Adam's first wife. Through these millenia Lilith has been cauterized until her soul and the soul of the tree are nearly one. Together their essense forms a great contingence that allows the God tree to reap life from the core of the macrocosm and the world of souls. Not any souls, only souls who have sinned greatly, they are the only with a mark great enough for the Lilith to grasp and harvest. In a final attempt to qwell the ever scintillating Lilith, the Yggdrasil incarcerated the Lilith's soul inside of a mortal soul, but Lilith's hold on the Yggdrasil was so great that it's soul was also sealed. The quintessence of the tree and the Lilith remained, glimmers and shadows of what they were yearning for their eternal souls. Without concious they are slowly drawn from the ambience of the world, bringing with them the renaissance of the world. The apokalupsis eschaton. But the corruption of humanity is too great, and like the cochroaches they crawl from their redemption to continue their debauched existance.  
The yggdrasil and the Lilith still yearn for their souls, their immortal sorrow ever so slowly tearing the dying earth apart. With the Lilith among them, the Mother of sin, sins of men has become less and less dilutted, condensing and manifesting into an infectious disease. Men with this disease follow the path of Lilith, causing their souls to be harvested by the Yggr in their death. Yggdrasil mourns it's subjugate to the Lilith and foreswears it's title as The Tree of Life. The people can feel it. The core of the earth is desintigrating. Little more than a shell of it's former self, Nageki no Ki, the Tree of Lament bends to the Lilith's will.
One asks... where is God? Where has he gone...? And the Lilith only laughs.