What?

Seriously, what?

Not bad, not bad at all.
Artist tried to tie the retconned universe to the current canon.

I think the artist was trying to get us to believe the protagonist was the current Marisa and it worked long enough. Because there's a part of you that'll go "Reimu is aloof but not that cold".
Calling that her "Kirisame" with that tone?
Wow, you could feel the indifference. Shocking, but that's where you start to suspect the twist.

Yukari, though, I can imagine her acting that way. She's unreadable to most characters, after all.

But what does human transmutation mean in this context, I wonder. Perhaps the artist was implying that current Marisa is a clone?

Im kinda confused about the author notes

So is that Marisa's mother or Marisa herself ?

Just...
Ya know what? No.

I'm still relatively new to Touhou so there's some stuff I don't understand. Am I correct in assuming that the person who looked like Marisa wasn't actually her and that her daughter was Marisa? Or are they somehow both Marisa?

Unrealistic, Marisa would never settle down with some random dude

Unrealistic, Marisa would never settle down with some random dude

I might be misunderstanding something, but it seems that wasn't Marisa but rather her mom.

That time when I had a nightmare of a Touhou Reboot

I'm still relatively new to Touhou so there's some stuff I don't understand. Am I correct in assuming that the person who looked like Marisa wasn't actually her and that her daughter was Marisa? Or are they somehow both Marisa?

Don't worry. I don't think any of us Touhou veterans were meant to understand it either. It feels purposefully opaque as some of its doujins are want to do.

Ooh wait...redhead marisa?...pc98?!? This could work

From what I'm understanding, this is following the theory that pc98 is a sequel to the current canon.
Windows Marisa broke a taboo (human trasmutation? Maybe her lack of fear for youkai led her to create a magic that could turn a human into youkai and viceversa?) and so Mima took away her magic powers (granted in this doujin her powers are derivated from Mima).
Without any magic she soon begun to greatly fear the youkai, so she probably went to Reimu asking for the Hakurei protection and setted down as a normal human, found an husband and had a child, Risa (pc98 Marisa).
Meanwhile Reimu has a successor (pc98 Reimu) and so the story goes; Reimu dies, Risa asks for power, Mima appears, gives her the power she took from Windows Marisa, and so we have a new Marisa (and this is the "reincarnation").

Wait so this doujin is trying to tie up PC-98 is the sequel to the windows canon? No wonder this is so confusing

I'm still not really sure what's going on at the start though. What exactly is this human transmutation magic and why did Marisa's power disappear?

I still like it, just a bit confused.

This was neat, but definitely a bit confusing. Isn't the Hakurei Miko (PC98) older than Marisa (PC98)? But unless I misread this story, Risa (PC98) was chosen to become the next Hakurei miko, before Mima gave her the power.

And yeah, Reimu acts super cold in this story.

Okay, here is my interpretation of the story.

Risa = Marisa Kirisame (Both PC-98 and Windows)
Risa's mother = Marisa's Mother
Hakurei shrine maiden (The one that disappeared) = Previous Hakurei shrine maiden
New Hakurei shrine maiden (Risa's friend) = Reimu Hakurei (Both PC-98 and Windows)

The story begins with Marisa's mum thinking about her regrets. She used to be a great magician tutored by Mima, who didn't fear the youkai. However, it lead to her destruction when she broke the taboo of human transmutation. Now she lives as a regular human in the human village, in constant fear of the youkai (such as Yukari Yakumo). When the shrine maiden disappears, she realises that she'll soon die to a youkai too.

Marisa's mum taught her daughter to stay near to shrine maiden, to be safe from the youkai she now fears.

Marisa, however, was inspired by Reimu's (the younger shrine maiden) power, and her Mother's fear of youkai. Thus, becoming a magician, tutored by Mima.

This story is basically about Marisa repeating the same mistakes as her mother. Just like her mother, Marisa now seeks power and doesn't fear the youkai, but eventually, just like it did to her mother, her power will be her downfall.
Marisa Kirisame is repeating the mistakes and the life of her mother, or in other words.
A Kirisame Reincarnation.