The thing is that all Gen actually wrote for the final scene in the script was "Homura alone, somewhere". The apocalyptic desert setting and all of that, that was something the animators of SHAFT came up with. That was somewhat the nature of this collaboration: a bunch of people just came up with whatever they wanted (Ume character designs; Urobochi script; Gekidan Inu Curry witch designs) and then SHAFT did whatever they wanted with them, lol.
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