Completely random speculation time:
It seems as though the plot is heading in a direction where there are several "alternate" versions of Eorzea that exist on shifted dimensions and that each of the Rejoinings/Calamities is the result of efforts to collapse these "fragment" dimensions back into "Hydaelyn Prime". Kidibus seems to be from one of these fragments, as are the WoD. The common link tying these threads together is our boy Eddy himself; he sees himself as an "envoy" of Zodiark. While the rest of the Ascians seem content to wreak havoc on the main Hydaelyn in order to forcibly collapse these dimensions, Eddy seems like he's taking an alternate approach, collecting strong survivors from these fragments in order to enact his more subtle plans. The lynchpin in this theory is, of course, if Kidibus is actually enthralled to Eddy or working on his own. We'll see I suppose.