As you all know, the Burst is now a part of the Chaos.
What happened ((storyline-wise)) is this.
Yggdrasill had become impatient, he wanted this world for her. First himself he layed destruction everywhere, using his odd energy. Then calling down his generals and lesser Angels came to conquer the Burst.
A long battle ensued between the members of the Burst and Cruxis, all seemed to be lost. That is untill the Proctors came for supports. The bought enough time for the Aircraft to be complete. Using the aircraft, I instrructed Neku, to take you all to the Chaos, I would stay here and fight.
During the battle much damage was taken to the Village as well as myself. Yggdrasill stood over my body after a long battle
Yggdrasill: You don't belong..in my sisters world!!
Right before a blow was dealt, Atomsk appeared before me
Atomsk: GO!!
Using a weird dark Burst he transported me, the NetNavi, the Zoid hangar and my lab to a section of the Nightmare.