What with the air superiority he seemed to have over the cities its a wonder why he didn't just beat dalamud to the punch.
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I'm sure they will be alive as Yoshi-P has said (will find quote) that the opening sequence and beginning storyline will explain what happened in the moments after the end of an era trailer and the fates of Louisiox and Co. The real mystery will be in how they survived. Its like watching the end of a cliffhanger TV show where the main Chr is laying in a pool of blood then the episode ends "Tune in next week for the exciting conclusion of End of an Era!" It would be like ending the first Iron Man movie after Tony got blowed up.
I like to instead entertain ideas on HOW they were spared. I heard Odin might have come in, that the beasttribes came in with their Primals and temporarily imprisoned Bahamut, among a few others. I think of the old "keys" on Dalamud there were more than 12, they were not just magic seals but technology enhanced ones. For the sake of the planet the Primals and Gods worked together with all the Citizens of Erozea to end the threat (some lore about Nael Van Darnus and the Ishgardians that I'm not remembering off hand.)
They alive just inside the crystal tower
The grand companies storyline with the circle of knowing, reuniting the three companies, and trying to stop Dalamud and such was live, one time only content for 1.0 players. So yes, that's getting scrapped too along with the original 1.0 storyline. We aren't getting any of the same missions in ARR.
And like I said, the essence of the story will remain, so the circle of knowing, grand companies, primals, beastmen, the Echo, Garlemald, Van Baelsar, the aftermath of Dalamud, Bahamut, these will all still be relevant in ARR.
The fact that it's "one time content" has nothing to do with it. It just means that it won't be playable, not that it won't be relevant to ARR's story. The fact that the content isn't playable has really nothing to do with what we're talking about here.
The only part Yoshida talks about when he mentions "scrapping" is the part of the storyline that was in the game at release, IE, most of the characters and organizations that appeared only before the GC storyline won't make a comeback in the new story. He's not talking of what will be playable and what won't.
Reading the original article (and not just a summary) makes it quite clear.