Theory with regards to the Justice League story in Batman Beyond Unlimited: Kobra is being manipulated by Apokolips.
While no one has directly mentioned Apokolips, there was mention of a "Genesis War" but not description of the fallout. Even if Apokolips was destroyed (and we don't know that it was), Beechen seemed to hint that at least some of the old baddies are still around in the pre-relaunch Batman Beyond ongoing. There was the man hired as the new worker's spokesman for Wayne's striking workers, who had some hinted connection with Glorious Godfrey. Beechen could have been running with the idea of the New Gods sustaining themselves inside human bodies, ala Final Crisis.
It could be Nguyen and Fridolfs are running with that. Apokolips lost that war, perhaps even lost their home, but they haven't given up, they've merely gone underground. It's hardly beyond their capabilities to get Kobra a text that makes a convincing argument destroying New Genesis is the key to restarting creation. And this way it looks like it's just Kobra being their usual world-ending selves, no hint of any force urging them on.
I suppose I'm just suspicious that the plan only involves destroying New Genesis and not Apokolips, since I sort of understood it that they were a matched set. Good and evil, in opposition, but also in balance. Though I suppose by obliterating one, you could throw the balance off, and things might then naturally spiral towards an end. Total and complete order, or absolute chaos.