Yeah, that's right. I'm trying to figure out what happened in the games. It'll probably be eternally a work in progress.
This is very long and fiddly, and largely pointless. I'll tell you my conclusion up front: the ingame stuff DOESN'T, in fact, fit together into a coherent canon. It's gonna have to be subject to interpretation, which most people do anyway. This is an exercise in being as thorough as humanly possible, perhaps in hopes of finding clues about how to interpret things. But frankly, if you already know Touhou, I'm not gonna tell you much of anything new that you'd actually care about, and if you don't then you have even less reason to care.
General Notes
For those of you just joining us, or who know nothing about this canon but are reading this anyway because it popped up on the network and you're bored, what is the problem here? Well, almost all games in the Touhou series have multiple playable characters who, in their scenarios, go through the same levels and fight all the same people and basically do the same things. (And the games that don't really aren't worth worrying about in terms of story.) So we come to the question of who actually canonically does this stuff, if anyone. It would be easy to say that Reimu just does everything herself every time because she's the main character, but aside from that being very unsatisfying from a character perspective, there are things that don't fit with it.
The most common strategy, though it's apparently been disproven now anyway, seems to be to take as canon whichever ending is labeled Ending No. 1, and thus whichever route leads to it. Of course, that would still say that Reimu does everything and saves the day every time except once or twice, but in any case there's stuff contradicting it. The other stray odds and ends that make reference to the games' events also provide a certain leaning towards Reimu resolving things. We can, you know, be pretty sure that she's involved in all this stuff. But it's also pretty clear that the other characters aren't just sitting on their hands doing nothing.
No, at this point I'm forced to accept that, on the whole, it's pretty much impossible to build a coherent canon using any of the ingame scenarios exactly as shown. Definitely impossible with some games. Which is not to say the basic outline of events can't be right; take it as a broad strokes thing. In my view, the most sensible option by far is to avoid the question. Hell, let's freely reference specifics from contradictory scenarios and completely ignore the inherent problems of it! It's not like anyone should expect Touhou to make sense anyway. Seriously, you can just stop reading now.
Oh, it's also common, incidentally, to portray the events of the games such that all the playable characters basically go through as a group. This is, quite obviously, not really supported by anything in the games (although, as I will note later on, it IS somewhat supported by a number of Extra stage prologues, yet not the Extra stages themselves or the normal game prologues -- very odd). It's a somewhat amenable approach since, again, I really have to assume that all the playables are doing SOMETHING. And I guess even if everyone investigates the incident independently, maybe they should be likely to run into each other anyway. On the other hand, maybe it's just me but it's hard to imagine them teaming up that easily, and if they are just encountering each other on the job it's a little more complex a course of events than that. Sometimes these portrayals will have the characters splitting up boss fights and such although sometimes that seems to be as much for the sake of shipping as anything.
If you want to continue, the next question is what actually needs to be reconciled. This definitely does not apply across the board, but in many cases, the various endings to a game don't actually contradict each other that much -- even bad endings often tend to indicate that the player character will just try again later. Marisa's endings in particular often have nothing to do with the actual game's story. And this is true even of the multiple endings per character in MoF (but not SA, where each route has distinctly different circumstances, and probably not UFO, where they have different motivations and dialogue). Also c'mon it's Touhou, there's rarely much more plot resolution than "the badguy stopped doing the bad thing and they all drank tea" anyway. Much of the time, the part that's really implausible is the gameplay -- that is, the sequence of bosses. Because there's really no need to beat Yuyuko up three times, let alone all those poor saps before her, and you'd think they'd mention it if they were having that bad a day. There's definitely no need to unseal Byakuren three times.
It's kinda something that the games themselves, the heart of the series, are less reliably canon than some of the other stuff.
As for other sources... Perfect Memento in Strict Sense discusses several incidents in passing during Reimu's article and occasionally others; but these represent the average human on the street's view of events, explicitly based in hearsay. Bohemian Archive in Japanese Red has full articles on all the incidents up till then, which are wayyy less useful than you'd think. They are mostly written while the incident is still ongoing, and follow the formula: 1) Aya becomes aware of something strange going on and decides to watch Reimu in case she does anything interesting. 2) Aya follows Reimu for a bit, but then gives up or is unable to continue. 3) Aya chooses to instead report her own baseless theories about the true nature of the incident and mentions that humans suck for not being able to enjoy it anyway. HOWEVER, those articles are also accompanied by very short little narrative blurbs that appear to be objective, so that's something.
...Jeez, Aya's been stalking Reimu since EoSD. Terrifying.
There are also a lot of other little references and occasional big references throughout everying. So, for the twin sakes of argument and knowledge, I'll put together everything I can find that points to what may have happened in canon.
As I mentioned at the start, this is of course all subject to change or otherwise continuing to be worked on. Input, analysis, and discussion are also quite welcomed; despite my tendency towards... er... thoroughness, I don't, in fact, know everything about Touhou. I mean, at this point I have my own conclusions about some things, but I'm perfectly happy to rework 'em for new information.
Embodiment of Scarlet Devil
The prologue says that both Reimu and Marisa set out to investigate separately, with no contact.
The Extra backstory has them both hanging out with Remilia and then setting off, more or less together. But neither version of the Extra stage itself contains any indication whatsoever of that. This is going to be a very common pattern for Extra stories and stages.
Remilia's scenario in IN mentions wanting to pay Reimu back for "that day." EoSD is the obvious inference; I'm sure it's possible (nay, likely) that Reimu's beaten Remi on other occasions, but it sounds pretty momentous and all. And it's not like they interact much, but there's been no indication I know of a similar grudge against Marisa or anything.
According to Akyuu, "it's said" that Reimu went to the SDM alone and resolved the incident. Aya's article has nothing to contribute beyond reiterating that Reimu went to the mansion, but her interview with Reimu indicates that Reimu claims to have, at least, done something heroic here. Anyway, that narrative blurb as well says Reimu went to the mansion to do something about it.
However, the Grimoire of Marisa mentions Marisa encountering spellcards during this incident. Only Meiling's, though, so I guess she could've gotten turned away at the gate or something. Or distracted by the library... (By the way, I know Marisa is a liar, but it would make absolutely zero sense for her to be lying in this context, so I'm takin' it.)
Perfect Cherry Blossom
Again, in the prologue, all three playable characters set out individually.
Extra backstory, too, has everyone hanging out at the shrine annoying Reimu. The three heroines play rock-paper-scissors to decide who'll do the Extra stage ("whoever doesn't cheat has to go"...); the results are of course not given. Then again, afterwards it kinda sounds like all three of them go again.
Oh yeah, in Imperishable Night, Yukari mentions she thought there were only three brave humans in the world, which is generally taken to refer to PCB's three playables. They wouldn't be brave if they didn't do anything, would they? And the context is even about being scared of her. Hm.
Akyuu also attributes this one to Reimu. She says that not much is known about this incident, and seems a little skeptical of Reimu's explanations, actually. Aya's useless. The narrative blurb says Reimu did something.
By the way, some believe that Yukari was never defeated in this game because she was supposed to fix the boundary to the Netherworld and it's still weakened. Personally, I'm indecisive about that; it seems weird to have the whole Phantasm stage be basically irrelevant with no greater indication than that, and I could probably believe that there's some technicality about the boundary or something. I don't know.
Immaterial and Missing Power
The prologue says that a single person starts investigating, but doesn't specify who.
Akyuu doesn't talk about this one. Aya does, and for once is useful since there's not much else about this one (even the blurb, this time, doesn't say anything about anyone doing anything). In observing the constant parties, she notes that everyone treats each other suspiciously (like in those murder mysteries where all the guests know one of them has to be the culprit, she alludes) but only Reimu really got that there was something wrong. Beyond that, Aya doesn't talk about what actually happened, ending the article while that situation's ongoing.
Oh, right, this is the one where Ending No. 1 is not Reimu's but Suika's, so it's often believed that she beat up everyone this time. Which works well enough, I suppose, even with the implication that Reimu tried to stop it (she's Suika's last boss, that's important enough!). Even Suika's ending still somehow resolves her incident.
Imperishable Night
Hooboy.
The prologue has Yukari setting out to recruit Reimu and Alice setting out to recruit Marisa. Remilia/Sakuya and Yuyuko/Youmu are more explicitly indicated to form up and head out. That's an interesting distinction because...
Despite that, Reimu shows up as a boss in the Marisa/Alice and Yuyuko/Youmu scenarios, and Marisa in Reimu/Yukari and Remilia/Sakuya. In both cases, the girl is completely unaware of the plot, and her possible youkai partner is nowhere to be seen. It's therefore unlikely that their youkai ever got ahold of them at all. ...But then again, Marisa and Alice show up together in Reimu's endings. Just what the hell happened here?
The Extra backstory is the usual pattern; the four human(-ish) heroines hang out, are advised by Kaguya to go do the extra stage, and all run off to fetch their partners.
According to Akyuu, Reimu claims to have solved this one, but refuses to give any details. This would be understandable for any possible course of events; the identities of the Eientei group are apparently being kept secret, and what most people think of as the incident was actually caused by the heroines in order to address the real incident nobody knows about. Aya mentions in one place that Reimu again claims to have done something heroic or other, and mentions elsewhere that it's rumored Reimu and Sakuya of all people were both involved in resolving it... that's interesting, since Sakuya/Remilia's route has Reimu as a boss. The article says that Reimu supposedly went on a rampage again, but that Aya herself didn't observe any of it this time; the blurb afterwards says only that major youkai worked with humans, no naming names.
Speaking of Sakuya involvement, I've seen it hazarded that the Scarlets may have won this one. Their good ending does kick off what became an ongoing project throughout canon to reach the moon. Which culminated in Silent Sinner in Blue, but is also the subject of a CoLA chapter and Sakuya's BAiJR article; the latter ties right into IN and, in fact, directly references that ending. To be absolutely technical, they could still all do that without having gone through the exact game scenario, but at the very least it's gotta support them having been involved...
Buuut the Grimoire of Marisa specifically claims that Marisa encountered spellcards during this incident. Wriggle's, sure, but also Reimu's, and worse, Eirin's. So she had to have fought all of them, or at least seen them all fight, during it. Um, hm, there's also a passing reference to IN in SSiB where Marisa mentions to Reimu that "we" teamed up with youkai that time. That's pretty vague, and who knows how much vaguer it was in Japanese, but to make any sense at all it seems like it should imply that one or both of them got involved complete with youkai partner... Maybe that's reaching.
...By the way, there's also the confusing fact that it's not actually possible to get a good ending in which the incident is fully resolved the first time you play through, it's more saliently not possible to do all stages in one playthrough, and since the plot's on a strict time limit there's certainly no way for one team to go through twice, even if that made sense in other ways. Yet more than one group doing it has the same problems as always plus the massive stage 4 boss issue.
This game is not going to make sense, the end.
Phantasmagoria of Flower View
Only Reimu is in the prologue.
Akyuu... who seems to know all about the nature of the incident anyway... says that Reimu set out to solve it even though that's completely unnecessary. Aya writes during the incident and agrees that Reimu's running around trying to fix it, and also that a lot of other people are active too ("I'm sure that some noisy nonsense will happen whenever they unexpectedly run into each other.") and the blurb again just says Reimu Did Stuff. Later in her interview, Reimu insists to Aya that she resolved this incident; Aya doesn't believe her story.
It may be worth noting, though, that at no point in this game does anyone actually resolve anything. Indeed, just as Akyuu says, the "incident" isn't even a real problem, and it essentially fixes itself a while afterwards. There's no real reason why everyone couldn't run around looking at flowers, picking fights, and getting lectured by Shikieiki. Even her and Komachi's scenarios appear to take place after everyone else's.
Mountain of Faith
The prologue has Reimu and Marisa discussing the problem, but only states that Reimu goes out to deal with it.
As usual they hang out in the Extra backstory. It certainly sounds like Marisa infiltrated the mountain at some point, as well as continuing to visit. And again they both set out.
PoFV was as far as Akyuu and Aya go, so that's all we got. Oh, but in SSiB, that is the parts of it that occur after MoF, Reimu's got a little sub-shrine for the Moriyas set up at her own shrine; this is specifically described in one of her MoF endings, although it could honestly fit with any of them.
Then again, this is another case where there isn't really an incident. The resolution (Reimu's) is basically "Hey Kanako, stop trying to steal my shrine" "Oh did you want me to ask first, I totally have a point though so let's work something out" "All right, now we've reached an agreement and everyone is happy" with some fireworks thrown in there at some point. Meanwhile, Marisa's endings in particular are especially irrelevant and don't really do anything for the underlying issue in the slightest, which is fair because there really isn't much she could do about it anyway. This is also one where the endings really don't contradict each other at all; I can definitely see both Reimu and Marisa individually going out to hassle Kanako and all the (good) endings occuring sooner or later. There are still too many real problems for the ingame routes to go together, though.
Scarlet Weather Rhapsody
The complicated one. It's generally assumed that all scenarios are canon, and they do seem to follow a timeline and reference each other. TECHNICALLY, though, it's still not possible for all the scenarios to occur exactly as shown without contradicting each other -- however, there are also cases where they very much seem to be portraying the same encounter in different ways. Of course, that kind of thing also raises further problems. And puts the entire already-shaky premise of this post further into question. Er, but anyway.
Subterranean Animism
The prologue is mainly Yukari and Patchouli talking. Yukari says that she will send Reimu to deal with things. (Would this make Patchouli's scenario the most likely of Marisa's to be canon?)
Usual drill for the Extra backstory; everyone hangs out, both Reimu and Marisa intend to go (this time they aren't specifically stated to actually do so). Incidentally, the Extra epilogue mentions Reimu having been made to go underground for the main game, doesn't mention Marisa.
Undefined Fantastic Object
This is an unusual case. ZUN has said, in a rather informal (rather drunk, but it's ZUN after all...) interview, that Marisa B's ending is canon. Surprisingly, this is still not wholly satisfying. First of all, nothing happens in Marisa B's ending, even by the standards of Touhou endings and Marisa's endings. It tells us nothing whatsoever that isn't also in the Extra backstory; for heaven's sake, Byakuren isn't even mentioned at all. For that matter, that ending doesn't even actually relate to Marisa going through the game at all, all she had to do was pick up a UFO at some point. It's not like I object to just saying that Marisa won the day for once, but, for the sake of argument if nothing more, I'll go over everything the same as with the other games.
In the prologue, Reimu and Marisa hang out; Sanae comes by and talks with them and then runs off while the other two suddenly notice the game's objective...
In the Extra backstory, Reimu and Sanae hang out; Marisa shows up all excited and shows them her Findings of Mystery, and all three go to chase after said mystery, probably individually from the context but it doesn't specify.
UFO is also an unusual case in that 12.3 and 12.5 make reference to what happens after it, shock of shocks. Byakuren starts a Buddhist temple at the human village, which is something addressed in several of UFO's endings, but there's no particular reason it couldn't have happened alongside the others. By the way, Sanae says "we pitched in to help build the temple" -- something like Kanako and Suwako helping with that in her A ending, perhaps? Nue makes nice with Byakuren and joins said temple, which follows from the dialogue in several versions of the Extra stage (but not Marisa A's or either of Sanae's -- though, again, I guess there's no real reason Nue couldn't do that anyway).
By the way, as always it's hard to imagine that two out of three heroines just sat on their hands while the other one did everything, but the scenarios aren't very compatible in this one. Even before Byakuren gets unsealed, there's a one-way trip to Makai on a magic spaceship-boat, which can't happen twice. Either more than one of the girls would've had to be on the ship together or the spares would have been unable to do anything past mucking around with Ichirin. (Maybe Reimu and Sanae were stuck with the demo version...?)
12.3 That looks kind of bad next to all the real names
Everything is almost certainly canon. There are only three story routes and they end up going in completely different directions without affecting each other anyway. (Plus it is an expansion to SWR.) However, one interesting note: the prologue contains a scene which is also in Sanae's scenario, but ingame the conversation goes on longer and (this being a fighting game) ends in fisticuffs. And one line that's in both is slightly different.
12.8
Your guess is as good as mine. But hey, it's not like it matters, the fairies have probably forgotten all the details themselves by the time the game ends. And there's only one Extra stage.
9.5, 12.5
These games don't even have multiple routes and nothing really happens in them except some tengu bickering anyway. Don't waste my time!
AHEM, what about PC-98, missy?
Yes, yes, I haven't forgotten you. Of course, there are differing opinions throughout fandom as to whether the PC-98 games are still canon at all before we can get into what's canon in them.
Really now, I think there are plenty of indications that they're still more or less canon. Alice and Yuuka variously recognizing/being recognized by the other characters, and other more oblique references here and there, sure. More straightfowardly, things like ZUN's statements on what's become of Genjii, and one of Reimu's profiles in EoSD says "Chronologically this title is not too far from the previous title, thus her age stays the same as before," which seems fairly decisive to me.
At the same time, there is also a lot of obvious mucking of continuity there. Everyone is different in Windows, everything works differently, the tone is more refined and the setting is more fleshed out in ways that don't always fit with the PC-98 stuff. But most of the time, it seems to me, rather than retconning it into "it's always been this way," ZUN seems to prefer just handwaving the differences away and moving on, "oh yeah that was sorta weird back then but anyway back to what's going on now".
We see this in the details of the Spell Card system and its established first use being EoSD; we see this in Yuuka who is "rumored" to have mellowed out these days; we see this in Makai's reintroduction being given the caveat that we're only seeing part of the place. In all of these examples, it's suggested that there is room for things to have been more PC-98-ish before, but the actual details are left completely unaddressed. Alice is a weirder case because combining everything that's said about her in both PC-98 and Windows gives her a strange history which seems like it must be awfully convoluted, although not so much that it can't be headcanonned together. But then, UFO dropped a couple statements about Makai which are so applicable to her I could kinda believe they might be deliberate hints -- again, without actually addressing the issue directly.
To play at psychoanalyzing the author, which is always a risky business, it always seems to me that back on the PC-98, ZUN just hadn't fully developed his ideas for Touhou, Gensokyo, and where he wanted to go with them; but he obviously liked them enough, and saw enough potential in them, to revisit them with more direction in mind. My personal impression is that he was willing to build on what he'd done before, but is not really interested in most of the earlier stuff in and of itself anymore. Well, that's my impression, like I say. My conclusion is the same regardless.
Anyway, regardless, it seems to me like a pattern of acknowledging the PC-98 games without worrying too much about the details. Which... is not actually that different from how it's going with the Windows games, apparently. But to my mind, Windows is the current focus and it has priority; where there are conflicts, PC-98 is the one that gets fudged a bit more. Because of that, and lord knows this post is long enough already, forgive me if I don't consider it worthwhile to go over the individual games. There wouldn't be much to say, anyway -- those certainly don't get mentions in written works, and we still don't even have translations available for many of the endings. (Although I guess Reimu in PoFV did imply that she beat LLS.)
So, in conclusion, nothing makes sense. Seriously.
I can't even be bothered to come up with headcanon on all of these yet :Dd. I do have my ideas about some of them, which I've probably indicated. I really have no clue what the christ happened in IN though.
Incidentally, I'm actually not really bothered by this mess at all. Even for the purposes of RP. I guess not knowing the exact events could be sort of inconvenient, but even when it does come up, it's usually perfectly acceptable to be vague. Besides, I play Marisa, she's full of it anyway. I also still have no problem making mutually exclusive references when it's not immediately obvious that there's a contradiction in them. Actually, everyone gets more dialogue this way, and that's more important for the purposes of characterization. (Although I give the games more leeway with that anyway, since they're stuck following a very rigid and stylized format, so... uh... well, anyway.)