This stuff is so confusing:
In WoTG it says that Robel came to the past from an alternate timeline in the future, as did Lillith and the other Spite wardens. A future reality where the shadow lord won and destroyed all the home nations, where Lilisette became the "john connor" of that world and lead a rebellion against him. However on the verge of being wiped out, she (or was it her parents before she was born?) made a pact with Odin (as Raogrimm did previously to become SL) to become Lillith. The Spite Wardens are warriors of that time that fought alongside her / them (and includes Robel-Akbel but he turned on lillith and his fellow spite wardens).
You travel back in time and so do they so there are two realities, this does not make much sense however.
From what I remember, is it:
The "bad timeline" is actually the real timeline and that you are in a "dream timeline" created by the Goddess Altana, that is on the verge of being destroyed by Atomos (cause it's fake).
So Altana creates the maws via Cait Sith sisters and sends you back (and they also influences other people like Lehko by merging with them) to make her dream Vana'diel into the real Vana'diel by manipulating the past, the characters from the real present see these maws (why were maws made there too? this makes no sense unless they are both linked) and go back to stop you changing the present.
Ultimately you do change the present and the real timeline is eras...well would of been erased but is saved as an alternate reality. However Lillith being now dead means the Shadow Lord would be the new ruler there and nobody rose against him, so Lillisette becomes Lillith to stop it being wiped out in a paradox......and if that happened robel and many others could not travel back to help you win.
As such reality is changed from bad to good and the bad becomes an alt world now, the dream world fades away.
However, if you are from a dream world and never existed outside of that, how are you still alive at all since you did not exist in the past or the bad present? I guess it's stating Vana'diel is a real place and you come into it from this another place (real life) and create your history in this world.
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In Rhaps, it starts off saying that Iroha traveled back in time, but as the cut-scenes progress the wording changes to a different timeline in the past. She keeps disappearing as you succeed in the story, which means a time paradox is destroying her from reality over and over again, and something (phoenix?) keeps resurrecting her continually. At a point Phoenix is destroyed or disabled and it cannot raise her again, so she is lost. From here Alexander? finds a way to let her live outside of reality somehow so that the normal paradox does not wipe her from existence. Some kind of time bubble or re-creating an alt reality again?
*** see Time Machine part at the bottom
At the end of Rhaps when you succeed, Iroha goes back to her barren dead timeline (implying Alexander? did make another duplicate timeline and that was how they solved her constantly being wiped) or did she go somewhere else? WoE?
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I get this kind of storytelling is really complicated, but it's also really complicated to understand exactly wtf is going on.
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I guess they were stuck in a situation similar to "The Time Machine" paradox
Inventor lost his wife to a car accident and that incident lead to him inventing time travel.
He then uses time travel to go back in time to save his wife and push her out of the way of the car.
However his wife dying is why he invented time travel in the first place, so if his wife never died how did he invent time travel? As such it's impossible to save his wife.