
Originally Posted by
Akoree
I'd have to look over at the cutscenes again but I'm pretty sure Dalamud itself is what gives Bahamut form through artificial "prayer". So that would mean that he's never been actually captured but rather given form in the cage from the get-go. This may also mean that the reason he disappeared after the megaflare is because Dalamud was no longer there to keep him "alive" and that is why the automated systems are now reconstructing him..
So far this seems the most plausible to me.
It looks like Dalamud was indeed created to keep Bahamut 'alive'. That is, weak but living. Feeding it just enough 'artificial prayer' to keep him in this realm.
Might be that when he broke free he might have had enough aether to sustain himself, but maybe he somehow lost that (due to megaflare?) and vanished back into the aether. Meanwhile the crashed remnants of Dalamud are still half functional and trying to resume their original task, thus slowly 'rebuilding' Bahamut (it looks painful and gruesome).
The other possible explanation would be that the crashed remnants were still semi-functional and somehow managed to recapture him, but I don't see how a bunch of broken shards of (admitted, very advanced) technology are going to capture a gigantic rampant dragon primal.