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").

Okay. Here we go.
I'm gonna try to explain this as best as I can. (Or at least as much as I understand.)

Separate timelines:
Timeline A: Marisa fails to convince Reimu to not use the spell of erasure. Bad future.
Timeline B: Reimu dies and takes Gensokyo with her. Marisa and Yukari escape to the outside world.
Timeline C: Marisa challenges Reimu to a spell card duel and kills her.

We'll start with Marisa A (our protagonist) in Timeline A. She is put in suspended animation and wakes up 80 years later. She goes to the shrine and meets Yukari, then goes to the woods and meets Reimu's great granddaughter (We'll refer to her as "Hakurei"). Eventually she realizes what happened and after Mima beats Hakurei, Yukari tells Marisa to go back in time and terminate Reimu. Mima throws Hakurei in after her. They end up in Timeline C.

Now, let's talk about Marisa B (black-haired, then short-haired Marisa). In her timeline, Reimu collapses Gensokyo just before she dies and Yukari pulls Marisa into the outside world. Marisa asks Yukari to send her back in time to try again. Yukari sends her to Timeline C.

Okay, Marisa C (the sleeper). She is put to sleep before anything happens.

The events of Timeline C: Marisa B arrives and puts Marisa C into suspended animation. Marisa A and Hakurei arrive and head for the shrine. Marisa B arrives at the shrine and finds Marisa A already there. She stays hidden and watches everything. Reimu has her meeting with Yukari and the Youkai scatter into the woods. Reimu is found by Aya and Nitori, who are then found by Hakurei, and then they all are found by Marisa A. Marisa A challenges Reimu to a duel and kills her. Reimu is brought back by divine intervention (by Mima being channelled through Hakurei). As a side effect, Reimu no longer remembers anything that just happened, including the spell of erasure. Hakurei promises never to use the spell, and is returned to Timeline A.

This is where things get tricky.
Marisa A goes home and finds Marisa C frozen in time. She is then confronted by Marisa B who plans to kill them both and become the "real" Marisa. Marisa B is pulled into a gap by Yukari and sent to the past of Timeline A. She finds Marisa A sleeping, but can't bring herself to kill her, so she simply freezes her in time. She then tries to convince Reimu not to use the spell of erasure and fails. (this leads to the bad future) She spends the next 80 years watching over the sleeping Marisa A while posing as Mima to blend in. 80 years later, Marisa A wakes up, goes to the shrine, meets Yukari, finds Hakurei, blah blah blah, and gets sent to Timeline C. Marisa B (posing as Mima) immediately dies because she's just so OLD.

As for Marisa A, now living in Timeline C...I guess she just lives life as normal, living in the forest, eating strange mushrooms, solving incidents, all while watching over the still sleeping Marisa C. (Which I guess would make Timeline C the new "official" timeline. Or at least it would if this story were canon, which it's not.)

Wow, that was a lot. Hopefully it makes sense. I really only understood it because I already heard another explanation on a different forum. Thanks, Shadowjack, wherever you are.

This is quite a nice explanation, but I have my own interpretation of the ending (or rather, beginning).

First thing first I think that timeline C gets visited 2 times: first at the start of chapter 4 when Reimu B gets transported to a parallel world (currently 2 Marisa there), and the second time at the end of chapter 3 with Marisa A returning to the past (3 Marisa there), so I think timeline A and timeline C are the same, but the changes that Marisa does in the last chapter "splits" them into 2 separate ones (in quotations because not entirely sure of this and depends on something I'll talk later)

So now let's start with Marisa B, going by the letter she has hidden in the journal, in her universe she sides with youkai and ends up killing Reimu, but as a last resort Reimu destroys Gensokyo and Yukari bails herself and Marisa to the outside world, just before the rainy season begun (Timeline B).
A couple of years pass and while she shortens her hair and dyes them black, she still can't let go of the past, so Yukari visits her and proposes her to return to the "past" through a parallel dimension where everything is basically the same (timeline C/A).
Here, her plan was to save Reimu and kill that universe Marisa (Marisa A) to take her place, so she put Marisa A to a deep sleep with drugs and cast a Za Warudo spell on her, dyes blond her dyed hair (lol), and goes to stop Reimu and Yukari from fighting (or not, not sure here, either way), and reaches an agreement with both sides, but she doesn't manage to convince Reimu to stop the use of the spell of erasure, so the next Hakurei shrine maiden still learns of the spell of erasure from Reimu and so on with the youkai slowly getting erased one at a time (timeline A).
Marisa B knew she could not change the time into a better one, so she went back to Marisa A's house to kill her, but couldn't muster the will to do it.
Feeling regret, she plans with that universe Yukari the plan to make things right: for 80 years she makes everyone think Marisa holed herself in her house, and so 80 years pass, Marisa B disguises herself as Mima, Marisa A wakes up and so starts chapter 1 (note: not sure if Marisa B visited the current Hakurei shrine disguised as a human Mima, which I'll call Reimu2, to tell her of youkai activity in the Forest of Magic or if she went there on her own).

Don't think I have to explain the stuff happening with Marisa A in the future, so I'll jump to when she and Reimu2 get sent to the past, there they return to the start of timeline C, and Marisa A kills Reimu.

Now here I'm not sure what happens with Reimu2, but I'll throw a random wild guess: Divine interference!
Something possesses Reimu2 and resurrects the dead Reimu while also reaching an agreement with her regarding the spell of erasure and leaves to "take her back to her home dimension" (I'm guessing by her it meant Reimu2) since the changes in time will make her disappear (here, timeline A and timeline C kinda splits).

So now, continuing on timeline C we have Marisa A going back to her home to find Marisa C (which is actually herself, just frozen in time), and the Marisa B that just got there trying to kill those 2 Marisa, but thanks to a last spell that the Marisa B in the future does (the Marisa that is disguised as Mima), she disappears (and so all Marisa B are gone).
Marisa A promises to find a way to dispell the Za Warudo magic and basically does the same as Marisa B did previously, only difference is that she wanted Marisa C to live in that time instead of going back.

Now meanwhile in timeline A, as the Mima disguised Marisa B disappears, Yukari meets what seems to be the actual Mima, but seems to actually be some sort of divine being (the Dragon God?) which by presumably divine shenanigans makes the erased youkai (or only Chen at least) return in that timeline like if nothing happened.

And I'm done, dear god, the more I wrote this interpretation the more I started questioning things...
Rinnosuke says that Yukari could at least only go to the past, and theoretically go to whatever future she desired since the future is made of infinite possibilities, but it seems the only thing she does is sending people to different worlds' past.
Also when Marisa A and Reimu2 went back to the past, they should've gone to their past since Mima disguised Marisa B said that they got sent in the world she got sent to, yet at the end Yukari says to the bathing Marisa she's from a different dimension... So I'm confused... Unless...

What if I read the letter wrong, and when Marisa B says she confronted Reimu two times it didn't include her own original timeline. which would mean that there's this world where she confronted Reimu the first time, but had to kill her again, and everything like her original timeline repeats (or she leaves before the destruction of Gensokyo) so she goes to the next and manages to save her, with arguably good results, here we have Marisa A and all continues as normal, but when Marisa A gets sent back with Reimu 2 they end up in this new world I just mentioned, so everything continues and this would mean that Marisa A is really in different world than her own and my head hurts.

Can say I'm done, doesn't help that I'm writing this while very tired and sleep deprived, but whatever, maybe this will be food for thought for someone to understand this story, or to get more confused by it...
(Please point out any possible error I made or theory of your own)

And so Reimu went and founded the most popular fast food chain: Miko Borgar

Pages 84, 86, 87, and 97 of part two make me grit my teeth. I'm not going back to reread the other parts which are just as atrociously out of character. I figured out what bothered me so much about this and the PCB remake after reading SSiB. They feel wrong. Every single character feels wrong. It's like they're acting correctly (sometimes) but the spirit behind their actions is out of phase with who they are.

Remilia going into a dramatic monologue halfway through the fight and making a big deal about losing? She doesn't care about losing, she's playing. A comment Zun made about Remilia in EoSD (technically through Reimu) is her danmaku showed "The tricky trajectories are kind of like a child trying to play just a little longer." The entirety of SSiB and SWR is her doing something because she's bored. And it's not that she doesn't care about Gensokyo or Reimu, but she'd never swear allegiance to them in this way. Like what the hell, she's dedicating herself to Reimu moments after meeting her? Because Reimu's her type apparently? That's just...

And Flandre, she's not insecure as she's mostly depicted here. In EoSD she's excitable, curious, and doesn't know when to hold back. She is not afraid of her ability, because she has never been given reason to.

Reimu's twisted the most. There's too much to comment. The entire story bends her into something she's not. What she is, is simple, lazy, foolish, greedy (but not really), kind while acting like she doesn't care about anything, observant, intuitive, accepting, strong friends with Marisa, and powerful without acknowledging her power. That's who she is, not this emotionless dreadnought. Oh yeah and calling on Amaterasu? That's hilarious too, considering how godless a shrine maiden she is.

...

I could go on forever but I'll save that for my myself lol. I don't know why the remakes are so weird. Most of their other works are really good. Maybe they just do comedy with a touch of thematic tension better? I'll just never read these two doujins again.

So, where should I start?
First thing first, all your sources didn't exist at the time, this doujin is from 2007.

Also because this is a doujin the author can take creative decisions, expecially at a time where the actual character appear in only a small number of official written works and more so in a franchise where the fandom was known to take characters and run with an extreme personalities just from a small line or just from some meme on a random forum (for some examples Reimu eating dirt, Marisa having a harem, Patchuoli and Alice having a love rivalry for Marisa, Aya being a pervert with her camera, Yuuka a sadist and Tenshi a masochist, and let's not forget Koakuma and Daiyousei, which they basically don't exist in canon, so much so their "names" mean "small devil" and "big fairy" and are called so because that was their entity name in the code, or even how someone was already drawing a doujin featuring Mike before the demo of 18 even came out and I guess all the ones where character magically have "mushrooms").

Lasty, it's ok to not like how the author interpreted them, but if your entire judgement on whenether a doujin is good is if they follow canon, then I'm sorry, but you choose the wrong medium to consume.

This is fixed now, sorry for the trouble. Enjoy your stay.

Yay, thanks

Sup, new user here.
So yeah, my insecure self used too much the preview post button and I got marked as spam. How do I get that removed?