The massive amount of energy unleashed by Noah's attack created a barrier that cut the entire battlefield in half. The tree suffered similar consequences. The black layer severed its trunk horizontally and divided the crown from the roots.
The division didn't affect the actual functioning of the tree. Both halves continued to work independently and express their nature by using the energy absorbed from the environment and the dragons. Still, Noah's attack destabilized the magical plant's overall structure, which inevitably led to a dispersion of fuel.
The trunk tried to bring its halves back together, but the dark layer appeared impenetrable. Energy escaped from the severed edges and spread through the void before falling prey to the many pulling forces in the area. Something vanished forever, but the tree managed to preserve most of its power.