I'm expecting a three way split, like in Shin Megami Tensei... I mean, like suggested in the first scene.
Kouta will acknowledge that Yggdrazil has a just cause, but he won't stand for their means, and, even if they cooperate a bit, he won't side with them. Kaito will be taken by Sengoku's faction which has no interest in saving the world, only in exploring the potential of the forest. Eventually they'll break up from Takadora's side of Yggdrazil. They might even ally themselves with the intelligent Invess later. Mitsuzane and his brother will stay with current Yggdrazil.