Primal energy fed to dalamud:
Atomos drains half the world- presumably goes to dalamud or void:
Garleans in dungeons feeding aether up- causes wildlife to go berserk crazy:
Main story hinted at someone riling up beastman to cause them to summon/get killed- more aether:
Midgardsomr incident slams into screws up aether at heart of eorzea- deaspected crystals appear:

so all that is removed from 12 and fed to bahamut- 12 cant beat a dragon aether junkie when hes full on tripping