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This is for Wild Mass Guesses about the PC-98 era of Touhou Project or characters from it. Wild mass guesses that involve works outside Touhou altogether go here. Ones that predict future games or refer to ZUN in any way go here. And the main Touhou Project page is for everything else.

Meira and Mima are the same person.
Meira is the Stage 2 boss in Story of Eastern Wonderland. She's never seen at the same time as Mima, she appears shortly before Reimu faces off against Mima with what appears to be the same goal in mind (that is, she wants Reimu's power), and she's never seen again. Sounds suspicious to me!

Shinki and Alice are...
  • Mother and daughter; Alice was actually created by Shinki, an "Artificial Child" if you will.
    • As a side note, since Shinki claims to have created everyone and everything in Makai, this would also make most or all of the other characters from Mystic Square her "daughters" in the same sense and Alice's sisters.
  • Foster mother and daughter: Alice fell down the metaphorical rabbit hole when she was young or a baby and was adopted by Shinki.
  • ABSOLUTELY NOTHING: Shinki and Makai were retconned out of existence.
    • The Makai still exists; no word on Shinki, though.
  • Renter and outsider. Alice was a human who had been training to magician-ship since childhood. Mid-training, she somehow found her way to Makai. Somehow, Shinki let Alice stay as long as she'd like.
  • Creator and creature: Shinki animated Alice from a doll, then Alice stole the power used to create her for herself.

Mima is...
  • Completely retconned out of existence.
  • Marisa's biological mother; this is somewhat implied by a music CD of ZUN's.
  • Marisa's teacher, and possibly a sort of "adoptive" mother.
  • The spirit of a member of the Hakurei family, possibly a branch member.
  • The goddess of the Hakurei shrine. She had been canonically referred to as like both spirit and diety.
  • The same soul as Marisa, from an earlier life. Bear with me for a moment here! Going from that same story snippet in a music CD that gives rise to the "Mima is Marisa's mother" theory, the reason people assume it to be about Mima is that the song it accompanies is one of her themes. But taken on its own, the story seems more to be implying the same thing as the title of the song states: Reincarnation.
    So what about the fact that Mima and Marisa clearly exist at the same time? Well, Mima is often referred to as a ghost, but she herself insists that she isn't one (and, in fact, denies being dead at all), while ZUN more commonly calls her an evil spirit. There has already been some distinction made in the Touhou universe among various types of lost souls and similar phenomena; ghosts, phantoms, and evil spirits are all different things. It's also been stated in Silent Sinner in Blue that a vengeful spirit can divide itself without lessening or otherwise affecting the original, and that this is essentially a characteristic of spirits or souls. Who's to say some part of a person's essence couldn't move on to reincarnation while still leaving something behind? Mima herself is said to have been an evil spirit for a very long time, so much so that she doesn't remember much of her own evilness. It's likely that she's quite different from whoever or whatever she originally was.
  • This troper holds the idea that one of the duties of the Palace of Earth Spirits is the capture and punishment of (even self-proclaimed) evil spirits. The reason why Mima hasn't been around lately? She's in detention at Satori's!
  • ...making the Touhou games. Whenever Zun says he feels "forced" to do something, it's because Mima is forcing him.
  • ...sealed away in the back of the shrine. Reimu finally sealed her up for good, and that's why she's made no Windows appearances. If Genjii can be "living in a pond behind the shrine" as an explanation for where he is, why can't something similar be the case with Mima?
    • ...sealed away in what we know as Rumia. Mima used mainly 'dark' magic, as does Rumia (albeit... in a much weaker form) in Touhou 6. Last time we saw Mima was in Mystic Square, first time we saw Rumia was in Touhou 6... Because Mima was too powerful for Reimu to seal completely, Reimu did the next best thing, and sealed Mima inside Rumia's hairbow. ZUN has already said that the fact that "Rumia's hairbow is some kind of seal" IS canon... coincidence or not, this COULD explain things...
  • ... playable in Urban Legend in Limbo and/or Antimony of Common Flowers, just nigh impossible to unlock. She embodies her urban legend by being an extremely secret unlockable character in a popular video game.

Byakuren is Shinki's form outside of Makai
See the similarities of the both. Byakuren even uses the same attack patterns as Shinki. Also, she brought one of her children again. And Myouren is a twisted Memory of her, which is in fact Alice Margatroid who was taken out of Makai by Force.
  • Byakuren was once a real human. When she was persecuted after secretly rescuing some youkai and sealed in the Underground, at some point, she made very good friends with Shinki and allowed her to use her identity. When Byakuran finally died, she gave Shinki all her memories and suchlike, so that Shinki could use her identity when travelling outside the Makai.
  • But remember that you fought Byakuren IN Makai...

The PC-98 games and Windows games take place in different timelines that are connected somehow.
There's several rather significant differences between the settings and characters of the PC-98 games and the Windows games - the appearant absence of the Spellcard Rules in the PC-98 games, the fact that PC-98 Reimu rides Genji rather than flying by herself, Alice originally being (or at least * looking* ) a lot younger than than Marisa and Reimu while she's implied to be a lot older than them in the Windows games, the presence of some high-tech weapons in the PC-98 games (Rika's tanks, Mimi-chan the ICBM) - but at the same time, there's also a few hints that the two settings/timelines are not completely separate continuities. One of the best arguments for this is the dialogue between Alice and Reimu in Perfect Cherry Blossom; Alice clearly reckognizes Reimu, and even asks her "Don't you remember me?" in a way that can only refer to their encounter in Mystic Square. Yet at the same time, Alice is - thanks to her backstory and mysterious age-up - * also* one of the best arguments for why the events of Mystic Square cannot have taken place in the timeline of the Windows games. The only logical explanation for this (other than this just being a mere Shout-Out, the Continuity Reboot being Lampshaded, or ZUN being drunk or not quite caring about the whole damn thing) is that the Alice from the Windows games timeline really is the same person as the Alice from the PC-98 games, but that she travelled from one timeline to the other at some point. The Reimu she meets in PCB is an alterganger, a counterpart from a parralel timeline/universe, of the Reimu that defeated her and Shinki. And exactly why did Alice travel to another timeline? My guess is that Shinki, being the loving (adoptive) mother she is, wanted to bring Alice to a safe place after her defeat at the hands of the protagonists of Mystic Square. So she created a portal to a timeline in which Gensokyo is a much safer place (thanks to the Spellcard rules, etc.) and, just to be on the safe side, she even went so far as to send Alice to a point in time before Reimu or Marisa were even born - hence Alice's mysterious age-up.

Zun never liked Mima in the first place
Fact: Mima was one of the most important recurring characters in the PC-98 games. Fact: Despite constant pleas from all the fans, Mima has not appeared in a single Windows game. Fact: The PC-98 games were created by a team of which Zun was a part, while the Windows game were all made by just Zun. Do I really need to explain this one? For whatever reason, Zun never would've brought Mima back for even a second appearance if the choice had been up to him, but it was not; it makes sense that now that he's producing works completely on his own he's not going to include elements or characters he doesn't like.
  • ZUN solely made the PC-98 games. Check the credits.

Sanae in Touhou 12 is really just Mima in disguise.
Here is the evidence. It also explains why she's so uncomfortable and powerful.

The PC-98 Reimu and Marisa are the mothers or grandmothers of the Windows ones
The reason Reimu looks very different between the two is because she's a different person, just with the same name. Mima isn't around anymore because she lost interest after the Reimu she befriended died. None of Yuuka's old exploits are in PMitSS because she hasn't done that sort of thing for decades now, but Reimu (w) still knows what she's capable of because of stories passed down the family. Alice's first conversation with Reimu (w) is the result of Alice getting confused by the colour scheme and some family resemblance.
  • Embodiment of Scarlet Devil's manual said "Chronologically this title is not too far from the previous title, thus her age stays the same as before." so...

Keine ate the PC-98 continuity.
Thus, things in Windows continuity can only indirectly reference PC-98 events and characters. Sadly, this theory would mean Mima is in fact gone for good.
  • Alice escaped by reincarnating herself as a human and becoming a Magician youkai. Yuuka escaped because she's Yuuka.
  • Alternatively, this is the origin of Touhou itself. ZUN inquired about a plothole Keine left from eating time, Yukari manipulated a few boundaries to find out, showed ZUN, then ZUN made Touhou, because it's not like anybody would care about time that's no longer here. After the PC-98 time ran out, ZUN moved onto current events, leaving the discontinuity caused by Keine's timenomming of PC-98-Touhou.
  • Another alternative is that ZUN was changing details to protect his source with Keine's help, which stopped being an option when goddess Rin Satsuki wanted attention (faith) from fans who could recognize her. However, since Keine wasn't informed of the change until too late, the two got into an fight which resulted in Rin's history with ZUN becoming altered, and subsequently her character was abandoned during the development of Embodiment of Scarlet Devil.

The reason Alice is so afraid of going all out in the Windows games is because of the events in Mystic Square's Extra Endings
Yeah, you're not misreading that; Mystic Square is the only Touhou game to have a proper ending and credits sequence (actually a list of all the characters in the PC-98 games) after its Extra Stage. They all involve some rather humiliating thing happening to Alice. Any pictures of young Alice being tied up or as a maid refers to these. Under that treatment, who wouldn't be worried about going all out? THEY MIGHT DO IT AGAIN!

Mima's true nature...
Mima is just a normal chick. I mean, she got killed eventually, but death happens to everyone, yeah? And she just so happened to be a magician, which, of course, isn't anything terribly special. So she's just died, and is minding her own business, sitting at the banks of the Sanzu River waiting for the lazy Shinigami to get to ferrying her across, when suddenly she's GRABBED FROM BEHIND AND DRAGGED OFF. (Explicitly stated as what turns one into an Evil Spirit, what Mima is referred to as) She, like any sensible person, Screams her lungs out, but Komachi doesn't even think of helping her. So, eventually, when she's completely within the bounds of the living world, she's got her powers back, and just beats the crap out of the Youkai that carried her off and kills them, explaining why she isn't under their control. Well, now she can't do anything to the one she dragged off... But, she's got no clue how to get back to the world of the dead. So she figures, she's not exactly "dead", explaining her dialogue in PoDD. But she realizes... She ain't going back. So her morals essentially vanish. That's what makes her "Evil". But... It wasn't her fault. So she wants to revive herself, if only to get a second chance. But in the meantime, she just wants to make the lazy ferryman's job as hard as she can- What the hell, I'm screaming and you just keep sleeping?-, and the only way she figures she can do that is just kill as many people as she can. Without morals, that's no problem to her conscience. It's not that she doesn't like humans, no! It's just, she has no value for life anymore. These people, they're getting a better end of the stick than her anyway! So she's just like, "It doesn't matter. I don't care anymore. Just make that Shinigami pay somehow... She doesn't even think of working!" SHE HAS THE SAME GOALS IN MIND AS SHIKIEIKI. SHE JUST GOES ABOUT THEM A DIFFERENT WAY. (Marisa got abandoned for using magic. She was misfortunate. Mima took a liking to her, so she became her teacher.)
  • This Guess deserves a Fucking Awesome seal of approval.
  • This is indeed a good theory and you should feel good.

The original Reimu, Marisa, and Alice were all killed shortly after Mystic Square.
In response to this, Yukari, Mima, and Shinki all went on a Roaring Rampage of Revenge and killed nearly all of the PC-98 cast.

Then Yukari kidnapped three girls from somewhere and used border hax to brainwash them into being Reimu, Marisa, and Alice— she missed the memo on Alice's age— resulting in the three almost-exactly-but-not-quite-entirely-unlike girls in the Windows games.

Mima and Shinki appreciated the gesture, but weren't comfortable with the Replacement Goldfish scheme, so they made Marisa and Alice neighbors for their mutual protection, then quietly abandoned them and receded from society. Out of loneliness, Shinki started teaching the imprisoned Byakuren some of her spells.

Yuuka survived the PC-98 massacre, but the experience and the loss of her servants and Mugenkan gave her a lesson in humility, which is why Windows!Yuuka has toned down the evulz, and is homeless and without servants. This might also be why Eiki rebukes her for having lived too long.

The new characters in the Windows games are new youkai moving in, or old youkai who made themselves scarce during the PC-98 days/slaughter and are emerging again.

The PC-98 games and the Windows games can be reconicled with each other
This is basically just me using WMG as a vehicle for putting down my various explanations, so here we go. Let's start with Marisa:
  • In the Windows games, one of Marisa's signature "signs" is the "Love Sign" series, which includes Master Spark and Non Directional Laser. Now, just from those two, you may think it's just for laser-style cards. You'd be wrong, as she has a few cards which are nothign but lasters that do not use any derivative of "Love Sign". Example: Light Sign: Earth Light Ray, and its upgraded form: Light Blast: Shoot the Moon. Love Sign isn't even used for all derivatives of the Master Spark: Once she reaches Final Spark, the supertitle has changed to Magicannon; similarly, Blazing Star is supertitled Comet, even though it uses a Master Spark for propultion.
    • Conclusion: the "Love Sign" supertitle is actually used for spells that Marisa steals. We know from canon found solely in Windows games that this is true for Non Directional Laser, and Master Spark derivatives only stop using "love" in the supertitle after they've changed so much as to not be even close to the original spell.
    • What does this mean for PC-98? Well, we know that Yuuka Kazami was the first character to use something like Master Spark: it was one of her strongest moves in Lotus Land Story. In Lotus Land Story, Marisa's self-stated goal was to steal Yuuka's power. Judging from her constant use of Master Spark in the Windows series, I'd say that she succeeded.
  • Speaking of Earth Light Ray: in Imperishable Night, ZUN's comments about the spell say that at this point in the battle, Marisa's been pushed to her limits; to the point that she's pulling out a really old spell. The spell is made up of thin lasers shooting up from the ground ad various angles. It is extremely reminiscent of Marisa's "extra attack" in Phantasmagoria of Dim. Dream, albeit modified to be an actual spell card pattern, and named.
    • This may sound like a far-fetched comparison, but then Phantasmagoria of Flower View came out. This being a Windows game, all the Extra attacks were named, and guess what? Marisa's is a copy of her Extra Attack from PODD... named Earth-Light Ray.
  • Next, let's take another look at Yuuka, shall we? In addition to supplying what is now Marisa's signature move, the oddly relocated flower youkai is mentioned in regards to Reimu a few times. In Perfect Memento In Strict Sense, Akyu mentions a rumor that Marisa once defeated Yuuka (though she doubts it). Whatever Akyu believes, there's no mistaking things when Reimu mentions having defeated Yuuka once before, when she talks to her in Yuuka's scenario in Phantasmagoria of Flower View. Yuuka may not have been talking about that at the time, but Reimu certainly remembers fighting her once before.
    • Conclusion: Well, barring the idea that there was some other big fight between Reimu and Yuuka aside from the one at the end of Lotus Land Story, it appears that this is a direct reference to said game, of which Yuuka was the final boss.
      • Problem: Despite the name, the incident in Lotus Land Story had nothing to do with flowers, and flowers were what was causing Reimu to accuse Yuuka of being involved.
      • Reimu says nothing about the flowers when she accuses Yuuka. She simply says "Everything went back to normal when I defeated you back then". Which is true. In any case, the Lotus Land Story incident involved a massive influx of evil spirits, which is sort of half of what the POFV incident is (overflow of spirits and the crazy flowers). Plus, Yuuka's newly-revealed identity as a flower youkai makes her all the more suspicious to Reimu. And nobody's ever accused Reimu of not beating up on someone for being very tangentally related to the incident.
      • Er, LLS was about large numbers of youkai (this being before youkai were established as the dominant species) coming out of nowhere, not spirits.
      • Oh, sorry. Misremembered. OK, so Reimu's reason for attacking Yuuka is downgraded to "she's tangentally related to the incident" (flower youkai) and "she's caused trouble in the past", which is about two reasons more than Reimu generally needs. In any case, I was never talking about Reimu's reason for attacking Yuuka; the important bit is that Reimu remembers fighting Yuuka, so unless this is a different Yuuka Kazami, with the same outfit, who has fought Reimu before...
  • Last but not least is Alice. She's a bit of a bucket of worms. Met in Mystic Square as a child in Makai, showed up again in Perfect Cherry Blossom as a grown woman (well, as grown as anyone can seem to be in this series). Not only that, but now she's described as a human that became a magician youkai, when it was initially assumed she was a Makai resident demon, like everyone else in Mystic Square. We can accept the idea that Shinki can make ordinary humans, or that Alice was "adopted" by her, if you will, but what about her age?
    • The explanation is in the Perfect Memento description of Magicians. According to said entry, there are three stages of being a magician: First is a completely human magician, who must cast magic through use of potions, reagents, and magical items. Marisa is one such magician. On the furthest end of the spectrum are "complete" magicians, who have learned a magic to abandon their "temper"; locking their age and extending their life. Patchouli is often regarded as one of these. In between the two is a transitional phase; occupied by youkai born as magicians, and humans who have learned a spell to become like said youkai. They can cast magic on their own, but still age and have a limited lifespan until they become "complete.
      • My theory is that Alice is one of these stage-two magicians. She has become a magician and abandoned her life as a human (or Makai-human), but she still ages, and that is the key. She appears to have aged between Mystic Square and Perfect Cherry Blossom because she is a Magician Youkai who still ages. She no longer needs a book to cast magic (though she still has it locked up and with her).
      • The problem was never that Alice aged, it's that she aged well beyond what should be possible in the time between the games. She seems to have gained a good ten years, while Reimu and Marisa are the same age as ever.
      • A growth spurt is possible, or perhaps Makai humans age faster. By the way, there are a pair of points I neglected to mention earlier. In Perfect Cherry Blossom, if you're playing as Reimu, Alice most definitely remembers Reimu. She calls her "old friend" and is annoyed when Reimu doesn't seem to remember her (perhaps because she's grown so much). Also, there's something about her book. In the intro to the "Grimoire of Marisa" Marisa says that the name is very definitely NOT a ripoff of Alice's. However, Alice's book is locked up and we can't see the title... except in Mystic Square, the PC-98 game, where we can see clearly that it reads "Grimoire of Alice". In any case, the book looks very much like the same one. In light of those two tidbits, I find it far more logical to assume she had a growth spurt/aged slightly faster than to assume that this is a different person, named Alice Margatroid, with the same book, who remembers Reimu.
      • It's also possible that... Alice didn't really grow all that much in between Mystic Square and Perfect Cherry Blossom, and it's simply a case of Not Drawn to Scale. If you look at Reimu and Marisa's portraits, or even the CD cover art, they honestly don't look much older than Alice, if at all, during Mystic Square. In PCB, she only seems much older because she's not wearing such childish clothes anymore.
      • Well, that and the fact that she acts like a young girl in MS, and like a reasonably mature adult in the Windows games.
      • Also, the only source that ever describes her as a human is Perfect Memento in Strict Sense. Every official profile given by Word of God never refers to her ever having been a human, and in fact, suggests otherwise. The article on Magicians seems to suggest that only the most devoted of human magicians can gain the skills necessary to become a youkai, which is something even Marisa hasn't achieved yet, but Alice's magical prowess is always described as average and even Akyu calls her a novice when it comes to magic. In fact, the official profiles always seem to make it a point to mention that she's a youkai as a species, calling her a "genuine magician."
      • Er, PMiSS makes a point of stating that magical knowledge has become easy to aquire, and that young magicians are now common.
      • Maybe she just used an age-up spell?
    • There's another, simpler way to explain away Alice. As established by dialogue in Undefined Fantastic Object, some humans and youkai alike travel to Makai to train and study because its environment facilitates magic (a fact that even resonates with the plot of Mystic Square itself, since Marisa's excuse for getting involved was to learn magic from Makai). This can retroactively explain Alice's presence in Makai during the events of Mystic Square; rather than being native to Makai, she had traveled there as part of her studies and training as a magician.
  • And there are my explanations of major bits of evidence, and explanations of seeming inconsitencies. Further investigation may be necessary on a few fronts, but I feel that's the most major points explained.
  • One last thing: Reimu explicitly mentions having gone to Makai previously in UFO.
    • No, no she doesn't. She indicates familiarity with Makai, but it's entirely possible she'd simply heard of it.
  • The first boss in Lotus Land Story was never actually named ("Orange" being a nickname from the game coding), so she might have been a younger Meiling, prior to her service with the Scarlet Devil Mansion— during which she was given a new uniform to wear. She's not used to the sedentary life of a gatekeeper, so she dozes a lot out of boredom and isn't very good at danmaku... but it's a step up from being a Stage One boss!
    • Orange's name does appear in materials other than the game's code. It's also present in the omake, and then appears during the Extra staff roll in Mystic Square when the names of the PC-98 characters are listed down, so it is indeed her name for all intents and purposes. Still, maybe she changed her name, or it's a case of I Have Many Names, or something.

Meira is a member of the Hakurei Clan.
She was after Reimu for the power of the Yin-Yang Orbs, right? Presumably she's smart enough not to chase powers she can't use herself, so she must be related to the Hakurei bloodline or she'd be seeking another route to power. Probably a more distant or illegitimate member, so she was ineligible to inherit the Orbs and the powers and responsibilities that go with them. She also shares (PC-98) Reimu's purple hair.
  • I'm hoping Reimu didn't know this when she assumed Meira was flirting with her.
    • Since she didn't know who Meira was, that's not likely. Or they're not very closely related; Kissing Cousins is okay in many parts of the world, including Japan.
      • I think she wants the Hakurei Yin-Yang Orb powers in order to enhance her own Orb powers.

Alice Margatroid and PC-98 Alice aren't the same person.
Just the facts: They look completely diffrent, PC-98 Alice' Last Name was never mentioned. Also PC-98 Alice is definitly a resident of Makai, not the forest of magic. The wouldn't be the only Touhou characters with overlapping names. (There are two Reisens) And it wouldn't be the only character using another one's theme. (Hatate uses Aya's theme from Mo F). I also think ZUN never implied that Alice Margatroid is from PC-98. Fanon just assumed that because of the name.
  • But in Hisoutensoku, one of Alice Margatroid's battle themes is "The Grimoire of Alice" aka the theme of Ex-Alice from Mystic Square. Plus, the locked grimoire she seems to constantly carry around resembles the one MS!Alice used in the Extra Stage.
    • That wasn't a remix made by ZUN, so it's unlikely to matter much.
  • This is pretty much denied by the fact that Alice clearly states in Perfect Cherry Blossom that she remembers Reimu ("Long time no see"), even if Reimu doesn't remember her. Why WOULD Reimu remember her? To Reimu, Alice was just another person in Makai she had to beat down. Even if she came back in her wonderland much more powerful, Reimu's defeated GODS before, so why should she care? YEARS probably passed between Perfect Cherry Blossom and Mystic Square. Alice, on the other hand, got her butt kicked twice by Reimu (and possibly Marisa) and no doubt held Reimu in her mind for all those years. Mystic Square Alice isn't given any backstory, only that she happened to be in Makai and saw fit to defend it. For all we know she could have been a human, grown up, and then became a magician youkai, migrating out of Makai and into the Forest of Magic. It IS possible to go in and out of Makai, as we see in Mystic Square and Undefined Fantastic Object.
  • Maybe the PC-98 Alice was Actually an Alice Doll.

Shingyouku is the manifestation of the Hakurei Yin-Yang Orb
I mean, think about it. Let's assume Highly Responsive to Prayers was Reimu's first time going out to solve an incident. Shingyouku F represents 'Yin' while Shingyouku M represents 'Yang'. On top of that, the theme song is called 'The Positive and the Negative'. It's quite likely that in order to test Reimu's worthiness, the Yin-Yang Orb became animate and turned into Shingyouku. Of course, Reimu isn't skilled enough to make THAT happen again.
  • I should also note that Shingyouku's first form is a ball. Coincidence? I THINK NOT!

Mima is the Saigyou Ayakashi sealed in a humanoid form with her memory gone.
What's the first thing Mima wants to do when she's unsealed in So EW? Kill every human /ever/. Her name means "Charming Demon," which seems very fitting considering the tree has the ability to charm people into dying. It's been said she has no idea what she is or how she got that way, so maybe she dropped the homicidal urges after forgetting. Marisa might have accidentally revived her, so she feels grateful to her.
  • Alternately, Yuuka is the tree. Or maybe both Mima and Yuuka are the tree, and are, as such, two spirits of the same being. It might explain how close they are before Mystic Square... Despite having never met before. Yuuka would be the "living" or "blooming" part of the tree, which would explain her... Violent tendencies. Mima, as I stated, would be the "spirit" part, and the "charm."

  • Perfect Cherry Blossom's deseal failure ensures that Mima is now stuck in the shrine for good. Yuuka may have lost some power at some point, or gained some, depending on how much spring stuck in the Saigyou Ayakashi. And if Sakura Nightmare was canon and Youmu beat up the tree.

Meimu is Meira.
Hear me out for a sec! Meira's original goal was to kill Reimu and steal the Hakurei powers for her own. At some point, Meira went "fuck this shit I'm taking an easier route!" and, somehow, succeeded in stealing the Hakurei powers. This caused her to change her appearance completely.

I am currently working on this very theory

PC-98 Gensokyo is another planet (or landmass) in space and ZUN retconned it.
The Probability Space Hypervessel is a spaceship. Reimu often finds herself flying across space in order to battle youkai.

This is why the PC-98 games contain so many star/space motifs, and why ZUN won't bring anything back from the PC-98 games. And finally, this is why UFO, the throwback to the PC-98 games, contains unidentified flying objects.

YuugenMagan was Yukari.
One of Yukari's spellcards is named after it in one of the games. Also, it's a set of five floating eyes that look suspiciously like the ones in her gaps. If it wasn't Yukari directly, it was definitely her doing.

Yukari used to be the goddess of the Hakurei Shrine. Mima has since taken over in her stead.
Yukari controls boundaries and borders, created Gensokyo, and placed the safety of the great boundary on the Hakurei family, who were her priests. But since Reimu has been... less than pious, Yukari has also fallen from grace and become a youkai, albeit an insanely powerful one due to her connections with the nature of Gensokyo. Her servants are youkai often portrayed as benevolent to humans, and sometimes even as helping shrines (the "beckoning cat" is in some retellings a nekomata).

In the meantime, Mima, who along with her servant Marisa was more into actually getting things done, has ascended to godhood as the "evil god of the Hakurei Shrine", and is now too busy trying to keep things working behind the scenes to put in any face time in the Windows games. Her grudge against Reimu is why Reimu remains poor, but she tries to send good things Marisa's way once in a while (though Marisa hardly notices sacred artifacts in her junk collection).

  • In Gensoukyou, Gods Need Prayer Badly is very much literal, so if Yukari was ever associated with the Hakurei Shrine itself she would have ceased to exist considering its complete dearth of worshippers. Yukari is also in the same "a youkai beyond normal youkai" category that Yuuka is in, making it even less probable that she is or was ever a god. Furthermore, Mima was never actually the spirit/god/whatever of the Hakurei Shrine, she just claimed to be such because she's an insufferable braggart and a chronic liar (something else Marisa stole from her).
    • Mima was sealed in a side-shrine on the Hakurei Shrine. Other than possibly explaining her lack of Windows appearances (Being stuck in a Hakurei-sealed box somewhere), this also means Mima would have to be secondary (Like Suwako to Kanako at the Moyira Shrine) to the Hakurei deity proper.

SinGyoku are Reimu's parents
Think about it. It appears at the Hakurei Shrine, takes the form of a Yin Yang Orb (a symbol associated to the Hakurei), a man, and a woman. Maybe they fought her to test her strength before allowing her to go to Makai/Hell, to make sure she was powerful enough to face the creatures she'd find there. After finding her power sufficient, they considered her worthy of inheriting the shrine, and left.

Mima is Geno
Think about it. People are always clamoring over wanting them in the new games. They're both spirits. They're associated with stars. They look sorta similar, too. Obviously they're one and the same.

Konngara was actually a human oni hunter turned oni
I recall reading that according to some Japanese legends, humans who defeat and kill an oni can turn themselves into oni by severing the dead oni's horn and implanting it into their foreheads. Konngara's title is "The Astral Knight", implying that (s)he is a warrior, and the blood on his/her forehead could be explained by the fact that (s)he implanted the horn in his/her forehead recently, and the operation was... messy. Of course, I might be mistaken about the humans-turning-oni folklore, but if it's true...

The First Hakurei is Mima and she became a Deity.
A quote from Danbooru: "I theorize that Mima was THE FIRST Hakurei miko (or the last one before Gensokyo was made) and killed herself with a knife because she fell in love in the human world and didn't want to leave. Which made her a vengeful spirit; vengeful against Gensokyo for almost taking her away. Which leaves one loose end...

The person she loved. Yuyuko Saigyouji. I think the two committed a love-suicide together under a sakura tree, and while Mima slit her throat, Yuyuko stabbed herself in the stomach. A stomach hole would turn her into a hungry ghost, and perhaps the suicide gave the sakura tree youkai-dom and created the Saigyou Ayakashi. Even if it stands against canon a little bit, that's my theory and I'm sticking to it."

Well, this is the base picture.

  • Yukari, a mutual friend of the two, realized what happened too late, but managed to free Mima by Windows-timeline and allowed Yuyuko to seal herself into the Saigyou Ayakshi once more by repeatedly hacking the boundaries involved.

Shingyoku is behind everything Yukari isn't.
Shingyoku could be the unknown Hakurei Deity (Appearance is actually relevant), and is simply pissed off from its own shrine maiden beating it up so early on the job, then stealing its sacred artifacts, then jailbreaking them, but allows her to keep the Orbs because Reimu is still doing the border maintenance and youkai extermination portions of her job. Shingyoku is only fine with Reimu not doing much shrine-related work from a total lack of worship, and thanks to Keine or whatever happened to PC-98 continuity has almost no faith. Byakuren and Rinnosuke are in on this, as are Yukari and Mima, but to varying extents. Yukari has hinted she's chessmastering against someone (See WMG above somewhere), and Shingyoku is so well-hidden nobody would know. Mima is stuck in the shrine again as of her last appearances, so it's implied Shingyoku could be telling her everything as she's about the only humanoid she can talk to. Genji is too busy being retired in the Hakurei Shrine pond to do anything, and Reimu is less than pious. Suika is just drunk and Yukari's too busy or thinks Shingyoku is nonphysical and maintained only by internet evidence of existence. The Moyira shrine is on the other end of Gensokyo anyways and they arrived later. Byakuren, mostly learning about this from Shinki, knows that Shingyoku is angry as hell, but not much more than Makai's goddess learned from the Hakurei Orbs when they were smacking her in the face with holy firepower. Rinnosuke just found and/or stole a book from the Hakurei Shrine that happened to detail who the resident deity actually was. The Hakurei Deity has been totally off screen since the beginning. Who's to say it hasn't done anything?

Maribel isn't Yukari
She's Mima. Upon discovering that Mima failed to cross the Sanzu River, Yukari started tearing apart the PC-98 continuity to find Mima. This caused Reimu's hair to change from purple to black, and caused the gates to Makai, Jigoku, and the Dream Worlds to be closed off. In fear, Rika and Rikako ran to the Kappas to hide, as they were fellow scientists, Meira fled back to... her samurai friends, Kana stops going outside her old house, Ellen, Chiyuri, and Yumemi all flee back to the outside world, Orange fled to the Dream World, Kurumi stayed where she was, as Yukari didn't care about her, and Yuuka's mansion was fine because Yukari didn't want to start a fight with Yuuka. Genjii and Ruukoto were taken by Yukari: Genjii because Yukari boundary-haxed Reimu the Power to Float in the Air and Ruukoto to make sure Reimu does her shrine maiden duties. With nowhere to hide, Mima had Marisa use a spell that reincarnated her as a human in the outside world: Maribel. And, since all the other plot holes were tied up, Marisa's hair changed from red to blond in between So EW and Po DD because of facing the magical power of the Yin-Yang Orbs. Yes, they are that awesome.

Every single PC-98 character reincarnated into a Windows character.
Mima doesn't show up because she's a completely different person.
  • Yuuka does show up, and I still believe Mima will show up again, and ZUN will play Reincarnation when she does show up again saying she has been Reincarnated to the series.

Mima is the retired/reincarnated/what-have-you Death Star.
Solely on the basis that the moon Mimas looks like the Death Star. And the fact that the Master Spark has been shown to destroy large areas when used right, and Marisa is using a hakkero instead of a giant power core.

Remilia and Flandre were originally Shinki and Gengetsu.
With Remilia the parallels are obvious: they both call themselves "The Devil," they both have a maid as their right-hand girl, their hair and eye color are the same. With Gengetsu it's more of a stretch, but her theme is "Cute Devil - Innocence" and they share hair and eye colors and appear in the extra stage. Maybe they were sent back in time by Sakuya, who Remilia stopped when she arrived back in the present. (See the below theory.)
  • Maybe they were originally Sariel and Elis?
    • And if one girl can become two, maybe Cirno and Rumia split off from them?
      • Alternatively, Cirno and Rumia are the real Shinki and Gengetsu, and in the Noodle Incident all their power wound up with Remilia and Flandre.

Makai and Hell were using Gensokyo as a battlefield prior to Touhou 1.
Mima is from Hell, and she gladly joined in the attack on Makai four games later. That would also explain the presence of youkai from both realms prior to Touhou 1.

Alice suggested the opening of tourism from Makai.
It was a plan to get the citizens out so she could hatch a plan to take over Makai. When Shinki told her Mima was coming, she left for the surface, leaving a doll of herself behind. This doll was what the heroes fought as the stage 3 boss. Then Shinki's attacks destroyed most of Makai, but some remained around the Alice doll. When the heroines were safely out of what remained of Makai, Alice detonated her double with such force that it destroyed what remained of Makai before Mima's evil energy could corrupt it. The seal on Byakuren survived both blasts as well as keeping Byakuren safe from the corruption.

Alice is actually Mima-operated dolls.
The Alice that we have seen in both PC-98 and Windows is/are just several different Alice-themed remotely operated dolls, all actually run by Mima. She simply had a self-discussion during Mystic Square stages 3 and EX in order to avoid arousing unwanted suspicion from the other side of the fourth wall that either Yuuka Kazami to the viewer or Yukari and by extension ZUN are to everyone. It explains why Alice would be friends with Marisa over the other protagonists she got beaten up by: It's because she's really Mima. Something unrelatedly dangerous caused all the major shift between PC-98 and Windows and not just the Vampire Incident leading up to the Spellcard Rules, a number of other small changes, and then whatever the hell with Rin Satsuki before the Scarlet Mist Incident, and Mima decided to hide somewhere secure and operate via her Makai proxy doll, Alice, who she edited or replaced and moved to Gensokyo to befriend Marisa. Alice having to sleep in her and Marisa's IN bad ending despite being a doll-like youkai is because something related to the Imperishable Night Incident busied Mima and the ghost thought up something unusually human in order to give her an excuse to stop operating Alice for a bit and focus on the other problem. The abandoned Medicine Melancholy being similar to Alice's doll type? She was either a prototype, or inspired the Alice plan. This also explains why Alice is constantly seen as Shinki's daughter over all the other girls in Makai: As a non-makai-originating ambassador of sorts to either Mima or Hell, depending on the exact canon at the moment, she would be given special treatment different from those that Shinki had directly created, and in Mystic Square Mima had shown that she could simply waltz out of some hidden Hakurei-brand shrine box and beat up everyone. The Grimoire of Alice and the EX-mode Alice was either an experiment of how the doll would work with a degree of autonomy and more magic power, a test of what would happen when push came to shove when Mima was not in ideal position to deal with the threat and Alice was the only option, or simply a test run of all the defenses and the charming demon everyone wants back is secretly hiding inside a fortress with the only entry being somewhere heavily defended in Makai. The Grimoire of Alice would also double as a communication instrument as well as a book full of magical power.
  • Smells like Voodoo Shark to me. First off, Marisa and Alice aren't always friends in canon; sometimes they're even rivals. Her dialogue in MS was about as friendly as that with anybody else (they weren't even friends back then), and her dialogue in PCB was arguably worse. Even her and Marisa's dialogue in IN seemed the least friendly. Secondly, there's a lot of Justifying in your WMG. Third thing, I'm in the middle of crafting a WMG about how Makai and Hell (where Mima came from) used to be an Evil Versus Evil rivalry.

Whatever made Makai an ideal place to seal things is no longer the case.
Lots of things were sealed in Makai. The entire Hokkai region and Byakuren, for one. Elis appears to escape a seal, for two. YuugenMagan, Shingyoku, and Sara all appear to be guardians of the way to and within Makai, and Sariel apparently being in a fallen shrine (which probably originally had Sariel wrapped up in an excessively thick shimenawa before she escaped and presumably destroyed the shrine in the process), for three and four. However, with Shinki getting beaten up in Mystic Square and the inhabitants doing things other than guarding judging by the same, and the defenses of Makai in the Hokkai area being unable to stop the Palanquin and protagonists from invading Makai to recover Byakuren, etc. etc., it doesn't seem that place is exactly as well-defended as it was when it was originally sealing things under guard by legions of demons, or everyone else just got stronger. Whatever the case, Makai is not exactly as good at boxing things up as it was a long time ago, and this will eventually be relevant. Maybe Shinki will get pissed off at Gensokyoans invading her land and start releasing everything inside?

Shinki likes to violently redecorate Makai.
There are lots of locations in Makai what with it being a whole infinite world of demons and whatnot, but they all look different, as if a hodgepodge of different designs were experimented with and the parts liked kept around. Notice how Shinki, the creator of Makai and presumably one who would make any large magical edits to the terrain, engages in a battle that is one of the few ones that actually manages to do a lot of damage to the surrounding area (by apparently burning down buildings), and by Mystic Square stage 6 some of the citizens were already evacuated by being on vacation or fleeing wildly from indiscriminately raiding protagonists, so...Why not, it's wild mass guessing.

The bloodthirsty ying-yang orb is of the same kind as the stage enemy ying-yang orb
It would explain why it is well more than happy to work with a youkai in attacking people. Presumably the teleportation powers are from a much rarer kind.

The Hakurei Orbs and the stage enemy ying-yang orbs are made of crystal from Makai
We know from PC-98 canon that the Hakurei Orbs are made of some form of wondrous crystal, and the stage orbs are probably the same. Makai is in some degree of proximity to Gensokyo, has enough crystal to make an entire fortress out of, and has sapient materials, some of which either naturally formed or were made into the stage enemies. Presumably some non-sapient crystal was used for the Hakurei Orbs or any user-hostile impulses were overridden by the Hakurei deity once they moved in and made it a go-shintai for youkai extermination.
  • As a corollary, this crystal has energy absorb-release capacities in general and not just with a god living in it, which is why they fire danmaku bullets as enemies and where Shinki got the energy to blow up her entire world while she was busy throwing everything she had at the Mystic Square protagonist. Presumably by the time of Imperishable Night, Shinki managed to get everything under control and was able to reopen whatever trade routes allowed said crystal to get to Gensokyo.

Mima is too busy keeping the Hakurei Shrine functional to put in any facetime.
Mima is the 'evil god of the Hakurei Shrine' after all. Consider the complete lack of faith from even Reimu (said shrine maiden wonders if even a myriad harvest god barely in season is as strong as the shrine god is) and near-absence of worshippers. Mima became an actual goddess at some point after the PC-98 era but before the Hakurei Shrine was portrayed in detail by the windows era, then had no real manifestation of divine virtues and whatnot because there's no faith to spare. With all of her regular evil spirit magical power being converted into something close enough to faith to keep the hakurei orbs hosting and Reimu's non-Reimu-based shrine maiden powers working by keeping the actual Hakurei deity not dead, she has no time to do things like wander about Gensokyo and get into danmaku fights any more. She's simply trapped at home by work.

Mugetsu and Gengetsu were Shinki's 'prototypes' for Yumeko.
They are demons with little explanation as to who they are, who live in a dream world that they created, which according to Genji the reliable Hakurei assistant turtle is on the edge of Makai created by Shinki, possibly to protect Makai proper from random invaders. They are very strong (being the extra stage midboss and boss characters), and one is dressed like a maid.

Yumeko lives in Pandaemonium, the capitol fortress of Makai where Shinki lives, presumably to protect her (Shinki is supposedly somewhat easier than Yumeko according to some YouTube runs, so Shinki may have actually needed/wanted protection in her servants), is very strong (being the Stage 5 boss and stated strongest creation of Shinki), and is a maid and dressed like it, with little explanation as to who she is beyond her role as Shinki's strongest creation and personal assistant.

Wild mass guessing time: The former pair was Shinki's practice for creating the latter person. They're oddly similar and the prototypes appeared before the final release, so to speak.

Mima is gone because Reimu got better at sealing things.
Mima repeatedly breaks out of her hokora side-shrine during the PC-98 days. She doesn't do so during Windows canon. Obviously, Reimu improved her box-making techniques and locked up Mima much better, and now Mima won't appear until someone releases her (probably Marisa or an incident) or the seal fades.

The Bathead's theories on what was going on behind the PC-98 era...
Makai (Demon World) used to indeed be Heaven, but then Elis came along and began to disrupt the order of the place. Iku managed to get her followers out before too long, but Elis was turning some of the angels into demons. Elis tried to summon YuugenMagan to destroy the dimension, but YuugenMagan refused to show herself fully. Once the new Hakurei came to the shrine, Sariel, the god of that dimension, caused an incident to draw her attention. Sariel managed to banish Elis to keep the seal on Yuuka as Gengetsu, but the damage was done: YuugenMagan had set Makai on a slow path to collapse, and Sariel was soon corrupted and began calling herself Shinki.

Mima was known for some time on the surface as a mischief maker, then she was banished to Hell for her deeds. But, naturally, she tried to take over and sealed the mistress of Hell as Kikuri. Kikuri's servant, Konngara, caused an incident to try and draw the new Hakurei's attention and make her attack Mima. But Reimu failed to completely destroy Mima, which would be needed to unseal Kikuri.

Later, Mima came back to life. Konngara realized she could use the Hakurei powers herself to destroy Mima, and so tried but failed to steal them assuming a guise as Meira.

Gengetsu secretly tried to break the seal on Yuuka against the other girl sealing her away, Mugetsu, and sent her ghost, Kurumi, to try and stop Reimu or Marisa from stopping Yuuka.

Shinki set up a "tourism" service to try and evacuate Makai before it collapsed completely. This drew the attention of Reimu, Marisa, Mima and Yuuka. Once Shinki was defeated, the dimension was mostly collapsed already, so she died with it. Mima sacrificed herself to preserve Alice's region of Makai and buy time for Reimu and Marisa to escape. Yuuka found her own way out. With Mima dead, Kikuri broke free as Satori. Without her mother, Alice soon left for the surface with Marisa. Alice's region would become stage 5 in UFO, and Byakuren was unsealed far below by the dimension's collapse, and just waited for her followers to come.

Shingyoku is/was the Hakurei Deity.
It is almost completely out of faith by Highly Responsive to Prayers, shown by the old-looking state of the yin-yang orb. Byakuren is aware the Hakurei Deity is angry for being stuck in such a state of zero-faith, but it can't really do anything but sit around powering the Hakurei orbs for Reimu, the only person who would even remotely care about its well-being at this point and doesn't even know its name. It also guards/guarded the gates to Makai and Hell, hence why having the Hakurei Shrine nearby for shrine maiden reinforcements and/or a decent home base was convenient and why establishing Gensokyo to keep the supernatural in that place was a good idea. Reimu actually did severely incapacitate Shingyoku during Highly Responsive to Prayers, hence why by Mystic Square Sara was placed by Shinki to guard the Makai gate. According to the vague descriptions of the road to the Sanzu River, Hell is probably unguarded completely or the entrance relocated. At any rate, being injured by its own shrine maiden and left faithless would be plenty of reason for a god to be angry, and with dangerous youkai partying around the shrine all the time driving away villagers for their own safety and keeping the shrine maiden's shrine maiden powers working is pretty much what it does now. Why Rinnosuke knows its name is not clear. Maybe he went to the shrine a few shrine maidens back and quietly stole a book detailing what the shrine god does?

The PC-98 characters are actually recovering from serious injuries.
Fact: the purpose of the Spell Card rules is to allow duels without causing death or serious injury.Fact: the Spell Card rules were invented between Mystic Square and Embodiment of Scarlet Devil.One can easily conclude that, before the Spell Card rules were in place, the youkai of Gensokyo (who are extremely difficult to kill to begin with) were, in fact, seriously injured.
  • Alternatively, they all escaped into Makai to flee the crazy shrine maiden and black white witch, except Alice (for Marisa) and Yuka (cause she's nuts). Now that Reimu and Marisa went back into Makai...
  • Or maybe they left in protest of the Spell Card rules.

Elly is a Scythe Tsukumogami.
Why else would she carry around what appears to be a horribly mutilated scythe? Even if the curve can be explained away by ZUN being unable to draw a straight line, why is it's blade sharpened the wrong way? It would also explain why she can boomerang it for no particular reason. If it's her real body, of course she can do odd things like that. Maybe her power involves telekinesis, sure, we can infer that from the floor tiles, but still. It may also explain how she blocks attacks with it. She's much more used to controlling her true body than her human disguise, right?

Gensokyo and Makai are locked in a cold war.
Since the fall of Pandaemonium in Mystic Square, the two lands have been separated by a hostile no-man's-land. The lock-step formations of Makai's fairies in UFO's sixth stage are due to the strict militarization that now dominates the land. It is also the reason Captain Murasa sailed the Palanquin Ship into a relatively unpopulated sector of Makai. She was trying to help the player character by attracting as little attention as possible from Makai's army.

Sariel and 'angels' like her are a Makai defensive grid
It explains the two angels in spheres in one attack phase and the background spheres in the opener, along with the star motifs of Mystic Square stage 2. The hole opened up into Makai by Reimu whacking Sariel in the chest and neck area with the Hakurei orb and multiple exorcisms is where Sara was defending, and the similar name is because Shinki didn't feel like being original about names that day. The gate into the fractal cave before YuugenMagan was the original entry in the mountains by the Hakurei shrine, probably closed after Reimu blasted her way in, and YuugenMagan was an advanced defensive system for that specific opening in the angel-star grid. They didn't show up in UFO because they were scrapped after Mystic Square by Shinki when she blew up much of Makai, because the Palanquin hopped dimensions directly and thus didn't use a gate, because Hokkai being so heavily sealed meant it didn't need to be defended that much or uses a unique defense like the Shinki-winged fairies, or some combination of the above.

Yuuka and Gengetsu are parts of a same being
Mostly from the contradiction of their names and apparent feature. Yuuka is associated with flower even though her name is an allusion of wind, while Gengetsu has bird wings even though her name is about moon (watch Futari wa Pretty Cure Splash★Star finale for better understanding of the allusions). In the idiom "Beauty of Nature", the phrase consists of the character of flower, bird, wind, and moon; four features of Japanese's traditional elements of self-discovery and, guess what, dream.

The two separated because of their differing ideologies. Flower and wind represent the earth, as in material understanding of life while bird and moon represent the heaven, spiritual understanding. Each created their own turf of dream worlds, perhaps as an attempt to understand their opposite's way of thinking. That's why Yuuka is a Blood Knight while Gangetsu is aloof, using Mugetsu as mouthpiece. Mugetsu is less a sister and more like a detachment of hers, an ability that Yuuka also possesses (also counting the Stronger Sibling younger sisters rule in the series; Gangetsu is older, and yet stronger.) also with Gengetsu's implication that she and her 'sister' can do Fusion Dance to be 'full-fledged adult'.

Reimu's courageous but stupid efforts in the first game set up most of the rest of the first arc.
When Reimu attacked Hell, Kikuri and Konngara lost the power to imprison Mima there, and she herself sought revenge and attacked Reimu's shrine several months later. Reimu's attack on Makai had far worse repercussions: Elis began a long plot for revenge by sabotaging Mugetsu's seal and awakening Yuuka, and Sariel's dark side took over in the heat of battle and she transformed into Shinki as her world began to collapse. The third incident, on the other hand, was triggered long before Reimu arrived at the shrine, as the outside world as mankind knew it began to collapse and many people began returning to ancient and/or eastern mysteries, among them Chiyuri and Yumemi.

If this appears in the WMG namespace on TV Tropes, I must have failed.
Long ago, humans put their faith in the dark creatures of the wilds in hopes of their mercy, and this allowed them to survive. But over the course of the past few thousand years, mankind have grown strong enough to keep their faith for themselves and their leaders, and because they were strong enough to fight the dark creatures, the creatures began to die off. Several hundred years ago, one elder being saw the love and beauty in the hearts of these creatures, and cordoned off a small country for them high in the mountains of the far east. They could not survive long without faith without coming into conflict in such a small realm, so this mad goddess brought together a small village of humans in the heart of the land to believe in them, but the humans quickly grew to fear all these strange creatures. They did try to fight them, but it was a desperate fight to stay alive. Over the centuries, as civilization drew nearer, this realm's author sealed it off through a shrine at the western end of the valley. The one shrine maiden had to pass it on to a successor before her demise or old age, or the barrier would shatter, leaving this small realm at the mercy of cruel humanity. But recently, just as this country seemed to be on the brink of destruction, a girl calling herself Reimu succeeded to the shrine. Reimu foolishly believed that she could wipe out the dark creatures from the country, not knowing that it was created as a home specifically for them. Even though she did not know the traditional use of the Yin-Yang orb, she invaded Makai, which had once been Heaven, and Hell. This accomplished little in the long run, but Reimu did soon learn the proper use of the Orb. She fought off invasions three more times, and participated in a great game in between. At the time of Reimu's first two or three sorties, I commented that they were nothing more than reckless actions, but in retrospect, they allowed this country to survive to today. Though, this did come at a price. Exhausted from her courageous but stupid efforts, Reimu became too weak to pass the shrine on to a successor, perhaps even to maintain it forever; at least her actions gained her immortality. Meanwhile, in faraway lands, people are turning back to ancient mysteries, granting many creatures of this land a new lease on life, and what's more, they are now receiving love rather than fear, allowing them to take on the faces of fair maidens rather than monstrous abominations. But in much of the world, dark creatures still face ignorance and fear, and with the emergence of hope here, one major group of them recently established themselves on an island in a lake at the edge of this realm. They are preparing an invasion force to take control of this village even as I write this. Even now, I see a few of them outside, on the village outskirts. I have set up ten defensive seals around the village to keep out the invaders. I hope this account will not be read by any tropers; it will mean that I have failed.

Yumemi is actually Renko's future self.
They're both physics scientists of Grand Unified Theory who adamantly believe the existence of the supernatural in spite of the world's view, their attires have many similarities, their general personalities are basically the same. "Yumemi" is also a quite ambitious name for someone who came from a future where "dream" doesn't exist. And also of all thing ZUN gives the narration of Renko and Maribel's Outside World situation, strawberry is the one that became the example of the extinct plant that only found as synthetic in their present.

The theory directly related with "Maribel is Yukari's past self" theory. Maybe when Maribel for some reason got spirited away by her power into the past and incapable of coming back to her own era, Renko grows obsessed of finding her. Just like when Maribel was diagnosed with hallucination because of her visions, Renko's attempt to bring light into the problem as first step to search for Maribel makes her a laughingstock. And so she creates the Probability Vessel to pierce through Gensokyo's barrier. Yumemi's action in Dim. Dream is to prove that Maribel is right and the Sealing Club duo are not deluded crazies.

Just like how Maribel arrived too far in the past, Yumemi's ship doesn't pinpoint the exact era she'd arrived in and stranded in a different part of their past because of some distortion of time because of the existence of Hakurei Barrier. The reason Yukari doesn't go down on Yumemi's ass unlike with Tenshi even though their actions directly disturbed the Hakurei Barrier is the same as why Yuyuko got away with her dangerous scheme without any sort of penalty; they're Yukari's friends, though Yumemi doesn't know it. And Yumemi still doesn't if we don't take the ending where she and Chiyuri became Gensokyo's residents.

Alice has a split personality.
One of them is the normal Alice (who isn't aware of any other personalities), the other is Shanghai (who is aware of Alice). When Shanghai is in control, she controls the doll as her main body, and puppets Alice's body, while making the "Alice" personality think that she's still in control. And yes, this means that Shanghai is the dominant personality, and basically supplies the Alice personality with fake memories of being in control.

The PC-98 era games are plays written by several people in the Windows continuity
Akyuu's Untouched Score is named such because, well, Akyuu owns the music in it - namely the full PC-98 score (plus unused tracks). And the back of each volume describes how, "many years ago in Gensokyo, there was a band known as the Yougakudan which dearly loved FM synthesis" and wrote songs using the technology. However, there are no in-character notes from the Yougakudan nor Akyuu in the scores, leaving a lot of room for interpretation as to why they wrote the BGM. Also, Gensoukyou has to have some sort of cultural produce that isn't related to stuff gapped in from outside, and culturally inclined people there would probably indulge in Write What You Know, too. So, playwriters wrote stories where the local shrine maiden and/or magician would save the day from their OCs. The Yougakudan were inspired and created music based on those plays, which eventually became more popular than the plays they were based on.

What would this explain? Well... Reimu didn't have a sudden personality change; the playwriters simply portrayed her as rather ditzy and energetic for laughs. Also, the writers were aware of Yuuka and/or Alice's existence (Depending on the Writer), but not the exact details like Alice's last name and age, or where Yuuka lived. They had also seen people battle using the spellcard system but were not aware of the exact details involved. Saying that there were several writers would also explain why there was so much more Negative Continuity in the PC-98 era.

Mima simply passed on
Mima is stated to be an Evil/Vengeful spirit, but each subsequent game had her becoming less and less malicious as she became more friendly with Reimu, eventually she let go of those feelings all together, which being a Vengeful Spirit also meant letting go of the thing that bound her to this earth as a ghost, this is not brought up by any of the other characters because its a completely mundane and peaceful way to go, the ghost equivilent of passing in your sleep of old age

Rikako, Yumemi and Chiyuri work at Kanako's nuclear facility
The Moriya Shrine crew may have already had familiarity with nuclear energy because they used to live in the Outside World, but being aware of it and knowing the very basics of how it works isn't the same as having all the knowledge of science and engineering required to run a power plant, especially one where a single mistake or oversight can lead to a large scale crisis or disaster.

But who would have such knowledge? Gensokyo's resident scientists, of course! They've been working behind the scenes to make sure the facility remains in good condition, runs the way it's supposed to and nothing breaks, malfunctions, leaks or otherwise gets out of hand.

Thanks to their expertise and diligence, there hasn't been any sort of incident or accident that could be blamed on the facility itself. The only times anything has happened have been either Utsuho herself acting up, or the publicity stunt with Hisoutensoku. While Chiyuri could be silly or clumsy enough to cause problems, Yumemi probably keeps some serious tabs on her for precisely that reason. Her ship and its resident robot maid ran on the same thing, after all, without anything going wrong.

As a bonus, perhaps Ruukoto also works at the power plant, cleaning up just like she used to aboard Yumemi's ship, and having her power source readily available within the facility itself.

The bakebake are drones
Now, I really wish I hadn't thought of this one, because it kinda ruins the bakebake for me, but at the same time it would make quite a bit of sense.

Remember how Rika said she created the bakebake? This always felt odd to me, and I tended to just ignore that claim because I thought it made no sense. How exactly would an engineer create ghosts? Unless... they aren't actually ghosts, but machines designed to look the part. After all, Rika also created Evil Eye Sigma, a flying tank designed to look like a winged big monster with a giant eye and a halo.

The fact they keep showing up for three more games but Rika never reappears might have been Rika trying to gather info on Reimu and her friends and enemies in a bid to come up with a way to defeat her in a future bout, but eventually determining she can't match her, giving up and thus the bakebake never appearing again.

Of note are the characters against whom the bakebake appear in Phantasmagoria of Dim. Dream. Mima fits because of the ghostly motifs, and Reimu makes some sense because they first appeared at her shrine, and because of Rika's short lived rivalry with her. But Rikako, the scientist, may seem out of place— unless the bakebake are themselves a product of science and technology.

Shinki changed the entrance to Makai
This explains why the characters get in aboard the Palanquin ship in Undefined Fantastic Object, whereas in Mystic Square the entrance had been inside a cave in the mountains. (It's entirely possible that Makai simply has more than one entrance, but let's assume it doesn't for the sake of this theory).

After the events of Mystic Square, Shinki could have been so upset at the trouble four of the strongest inhabitants of Gensokyo proved capable of leaving in their wake throughout Makai (she even explicitly begs the player character after her boss fight to never come back) that she decided to make it harder to get in, did away with the portal inside the cave in the mountains and instead created the entrance that was later used by the Palanquin ship.

This does beg the question of why she didn't just seal Makai off from Gensokyo entirely. One possibility is that she simply can't do that (maybe Gensokyo and Makai have some sort of special connection that requires them to always have direct access to each other, or else things will go wrong). Another is that she needs access to Gensokyo for her own purposes. Perhaps there is important trade between both realms, and the new entrance is strictly managed so that trade can continue but no one causes a stir. (This probably isn't entirely foolproof, as UFO demonstrates). Since UFO establishes that magicians go to Makai as part of their studies, maybe she understands how important travel between both realms is for the study of magic, and tries to ensure that the way in is only known to magicians, but Byakuren's followers found out anyway. (Despite being a magician herself, Marisa is probably left out of this loop on purpose because she was one of the "troublemakers" in Mystic Square).

It also begs the question of how Byakuren's followers, who had been stuck in the Underworld for ages, knew how to get in if the current entrance was only created recently, albeit they probably got the intel on that from a privy Gensokyo inhabitant (perhaps Alice?) offscreen. Besides, theory or not, the chances the entrance hadn't changed before in the long time since they got stuck down there are low in any case. Or perhaps the current entrance is actually an old entrance being reopened, one that existed before the portal in the mountains was ever a thing; Byakuren's followers simply took the entrance to Makai as it was back before Byakuren was sealed, and it just so happened to be the entrance currently in use.

Elly is a shinigami
This theory mostly just builds on the subtle, obscure cultural inspirations underlying the character of Elly, but adds to them by showing how it also highlights Yuuka's badassery in the process.

Elly is based on Ankou, a figure from Breton folklore that is akin to The Grim Reaper. Ankou wears a hat and carries a scythe just like Elly does, and her theme is named "Perdition Crisis", where perdition refers to the Christian concept of damnation. Brittany is known for its cider, and cider is made from fermented, or would you say, bad apples, thus explaining the title of her stage's theme.

Meanwhile, the modern concept of shinigami was strongly influenced by the introduction to Japan of European depictions of Death (in fact, The Grim Reaper is often referred to as "Shinigami" in Japanese media), so it's not hard to make the connection for how a character based on a European representation of Death would be a shinigami in the Touhou universe.

This also emphasizes how powerful Yuuka is, seeing as she has a grim reaper working for her as her mansion's gatekeeper. (Think of it like how in Castlevania, Dracula is so badass as to have Death as his right hand).

To this last point one might argue that Elly is a Stage 3 boss that got thrashed twice in a row and thus can't be that powerful, but it must be remembered that 1) Stage is not always indicative of power (for instance, ZUN has noted that Letty, a mere Stage 1 boss, is actually strong enough to start an incident if she wanted to), and 2) Elly was out of practice due to a long time having passed since she last fought— at the top of her game, she might well have been a legitimate threat, and it's not hard to see how being rusty could set you up for such a beating when your opponents are Reimu and Marisa, two of Gensokyo's biggest guns.

How Marisa developed her Master Spark
It's well-established Fanon that Marisa based her Master Spark on Yuuka's giant laser from Lotus Land Story (or alternatively, on Gengetsu's giant laser in that same game's Extra Stage). However, there's more to it.

Going off the prologue to Mystic Square, it's strongly suggested that Marisa's motive for going to Makai is to learn magic (albeit in her ending she keeps making up other reasons for her involvement in the plot). Her ending establishes that she got stronger and gained knowledge from her trip to Makai, and her bomb in the game has her shoot a narrow laser forward, which could be interpreted as a precursor to Master Spark. Master Spark proper then made its debut in the next game, the Embodiment of Scarlet Devil.

The theory is as follows; Marisa did get inspired by Yuuka/Gengetsu, but at first didn't succeed in replicating the giant laser, only being able to produce a narrow (if still strong) beam by the time of her campaign in Mystic Square. However, that trip gave her both the knowledge and power she needed to finish developing her laser spell, resulting in the Master Spark we know and love by the time of the Embodiment of Scarlet Devil.

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