Here's WNSP v1.02α, which contains the Extra stage.
You can transfer your previous version data by copying the "data" folder from root/script/Th_wnsp into the same place in the new version.
And, since the spoiler guidelines are no longer in effect, this is the solution to the mystery so Extra can be unlocked:
PART 1 - Timeline
PART 2 - Culprit
I haven't played the Extra yet, so etc.
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Having played the Extra--
WNSP was received as a meh game but I think the Extra stage was worth the experience. It's really pretty, and it makes good use of the mechanic. The difficulty goes up quite a bit for the last part, but I just barely failed on my first run because the tactical bombing mechanic gives you so many resources. I sense that the boss attacks are mostly easier than they look, but you still have to take them seriously.
Also, the fifth and tenth spell cards are different based on which protagonist you're using.