These final fantasy stories always involve nature vs technology. gaia vs man, lifeforce vs using the lifeforce to power factories and weapons.

Dalamud is the technology (and the garleans). The natural world is made up of aether and primals and the twelve, right?

Most likely Cid will find a way to use the aether (lifestream~~) to stop dalamud, possibly damaging the lifestream in the process, disrupting the land, etc etc.