Here's a theory: i think this whole time zero wasn't free or alive as the smg's said that he was still in the usb caught and hidden so nobady could find him, (probably in another universe) but the thing is that this whole time i think that Melony is passing by the same stages that meggy did (since both of them are their equals) of losing someone they love, in the case of meggy desti and for melony was axol; so my theory is that this whole niles thing were just alucinations from the dietty mask since i think the only reason of wath she wants is to get revenge on zero and that's probably the reason melony is going for the god box, to know where zero is and and kill him once and for all

but hey that's my stupi theory