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Originally Posted by Qaenyin
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The canon answer for this one is that what happened during the hollow ataraxia game was inside a reality marble so it happened in another dimension or a parallel universe.
The canon story line of Bazett Fraga McRemitz original lancer master is that Kotomine Kirei betrayed her and stole Lancer's command spell by chopping off her left arm during the 5th grail war.
She survived 4 more days after the incident but was left to die in the church basement and she actually died but remember that the grail system is a path to the origin and its where all the souls go back when they died, at that moment as we know from the FSN game the grail was already corrupted by angra manyu and the path to the origin was already semi-open. The premise of the hollow ataraxia game is that avenger came in contact with her once she died offering her a second chance.
That second change is impossible in the same time stream or universe as the FSN game develops and their endings.
that's why everything that happens with Bazett happens on an alternate reality just like tohsaka was taking the prana from other realities while she was attacking with the Zeltretch sword/dagger.
In short, speaking about the time line that exist for the fate zero story as well as for the time line for FSN, Bazett Fraga McRemitz, former lancer master during the 5th will have her left arm chopped off and left to die.
This is how this dots are connected to fate/zero as well as FSN franchise.