It never actually came out of the blue; the battle had merit because it was alluded to during the Dark Masters' arc, when Apocalymons' presence twisted the Digital World -- the four ultimate-level bad guys had also been feeding off this for their power-grab. His origin is quite plausible in the universe, too, having been manifested from deleted digimon either killed or failing an evolution.
I'll have to agree with 02s' epilogue, though. That certainly raised more eyebrows than needed.