Part 57SA Prologue
Like IN, SA has a prologue from the viewpoint of the protagonists and an actual prologue hidden in the character profiles.
Snow falls on the Hakurei Shrine in winter.
It had been destroyed by an earthquake before, but now it's back to normal.
Remember Immaterial and Missing Power? Touhou 10.5 (Scarlet Weather Rhapsody) is its successor, and it's set between MoF and SA. It doesn't really play any role in the events though, so Sanbondo didn't bother including it in FMW3. But the fact that it's even mentioned in the prologue is noteworthy: following MoF, ZUN tried to make the plots of all the games a little more interconnected.
One day, something happened to surprise the Hakurei Shrine's shrine maiden, Reimu Hakurei.
That was the sudden appearance of a white pillar shooting into the air - a geyser - near the shrine grounds.
Normally, when something unusual happens, she goes to find out what happened and quickly bring the matter to a close, but this made her happy as much as it surprised her.
After all, the geyser would melt the snow and become a hot spring that would ease the fatigue of both humans and youkai from nearby.
Anyway, SA starts with a geyser suddenly shooting up behind the Hakurei Shrine. Reimu hopes it'll become a hot spring that'll attract visitors, but before that can happen some vengeful spirits start shooting out. Reimu and Marisa take a look at this, shrug, and build a spa anyways.
Needless to say this is a lot different from FMW3, where the hot spring is built first and then evil spirits rush out.
The Scarlet Devil Manor
The magician that lived in the Scarlet Devil Manor, Patchouli Knowledge, sensed danger in the appearance of youkai and earth spirits from underground.
In her readings, she'd learned that somewhere slept a power that was uncontrollable by the likes of the youkai from above ground.
She also knew that youkai shouldn't easily be able to enter the city that lay in the depths.
However, there was almost no-one she could consult with regarding this problem.
Losing her temper with Reimu and company, she grudgingly decided to consult with the youkai who was said to have been in Gensokyo the longest.
Surprisingly, the main figure behind Reimu and Marisa making their move is Patchouli. She meets with Yukari and convinces her to do something about it (or to be more exact, Yukari decides she should do something before the SDM screw things up again). This being Yukari,
Yukari promised only to send Reimu to investigate, with youkai staying behind to act in a support role.
Reimu is promptly sent out. This is another game where it doesn't really make that much sense to play as Marisa.
It's mentioned in the prologue that only humans can go to the Underworld. FMW3 justifies this with an agreement, but the actual SA prologue only notes that Yukari didn't want youkai from the surface to interfere with Underworld affairs. She's also worried it might just be a trap.
...No, I've already reached my own conclusion. I'll be accompanying you to the Underworld. And I ask the other youkai to lend their assistance as well.
FMW totally drops this because otherwise the player would be stuck with barely anyone, and after SSiB already limited your party that would just be a huge dick move.
FMW also dramatizes the hell out of Yukari's relationship with the Underworld. It's portrayed as one of her many regrets, a big black mark on her dream of a Gensokyo where everyone gets along. Said dream is totally made up by the way, and in fact the Gensokyo portrayed in FMW is noticeably lighter and softer than the real one. But that's off-topic.
While only Patchouli and Yukari were mentioned in the SA prologue, Reimu and Marisa both have three possible partners. Their respective motivations are:
Yukari: Wants to know what the hell is going on.
Suika: Yukari got lazy and asked Suika to handle it for her.
Aya: Same, but Aya volunteered or something. She's been following the gossip on Youkai Mountain and is aware the Moriyas did something underground.
Alice: Her dolls were being possessed by the vengeful spirits near the hot springs so she was worried.
Patchouli: Figured Yukari wouldn't do jack.
Nitori: Is aware that nuclear energy is down below and wants at it.
One day, [Orin] felt a disturbance in what was left of the Hell of Blazing Fires.
The flames were much stronger than usual.
Regulating the flames was Utsuho's job. Orin went to visit Utsuho and was surprised by what she found.
She had discovered a frighteningly strong power, or had been given it by someone.
Since then, Utsuho began to grow stronger, and to seek out power.
Eventually, she started talking about conquering the above ground and turning it into a scorching hell.
There's no way she should have been able to do that. There's no way Satori would allow it.
If anybody underground found out about this plan, the oni would probably take care of Utsuho.
Amazed by the transformation her friend had undergone, Orin began to delve into a forbidden art.
That forbidden art was how to drive the evil spirits above ground. If she could force some sort of incident with the youkai above ground, something would surely change.
She was trying to get the youkai above ground to help her, but what finally appeared before her was a human from above ground.
That human was unexpectedly strong, and what is more, she specialized in youkai extermination.
If she's really that strong, Orin thought, she might be able to deal with Utsuho.
Anyway the real prologue is that the Moriyas bestowed Yatagarasu to Utsuho, who went nuts. Afraid for what might happen to her friend, Orin sends spirits up to the surface in hopes of attracting attention. This is exactly mirrored in FMW.
SA Stage 1
Stage 1 sees the player character of your choice descending into the Underworld. She beats up Kisume and a bunch of rocks, and in between bitching at her support partner and making silly one liners she smacks Yamame too.
FMW3 has this running tangent where Yukari tries to peacefully convince the Underworlders to let them go through, but it never works. Sanbondo uses this game as a chance to let some of the lesser characters get their time in the spotlight, so Wriggle tries to make friends with Yamame and Nitori realizes she's being kind of a jerk.
SA Stage 2-3
Parsee is pretty much just a roadblock on the way to the Old Capital,
while Yuugi runs into the protagonist in Stage 3 and ends up getting interested in her. She's the first person to actually be important, and she directs the protagonist to the Palace of Earth Spirits.
Oh, and in most of the routes this is also the point where the protagonist actually finds out why she was sent underground. She isn't very happy she has to shut down the hot springs.
Meanwhile in FMW, Parsee and Yuugi are basically dating so you fight them both at the same time. You never even go into the Old Capital, or at least not in gameplay.
Yuugi's a bit interesting in that while most of the Underworld are unhappy with their situation but see no hope, Yuugi and presumably the rest of the oni are totally cool with chilling underground forever. Since Kaguya's big thing this game is deciding to go outside, she is naturally less than accepting of this mindset. Suika is there too.
SA Stage 4
The protagonist makes it to the Palace of Earth Spirits, where she fights Orin for the first time and then run into Satori. Who proceeds to show off the real reason people hate the satori: because they won't shut up about the fact they're reading your mind. Kind of hard to hold a conversation when you keep getting pre-empted, you know?
She fights the protagonist out of self-defense, and after the battle notes that they didn't actually have to fight. She pieces together that Orin is probably the one behind the spirits, so she sends the protagonist on their way to the Remains of Blazing Hell.
Satori left Orin in charge of the evil spirits and Utsuho in charge of the Hell of Blazing Fires. They were both loyal to Satori, so they shouldn't have done any harm. She believed there was no way they'd start some sort of incident.
...Which is kind of weird, since Satori's profile states that she's pretty confident in her pets' innocence.
This is what FMW Satori goes with, to the point she fights the party over it.
Satori's entire situation with Koishi is much more dramatized in FMW. In the source game all we know is she pities Koishi.
SA Stage 5
Stage 5 sees Orin fighting the protagonist two more times, in what is apparently a test to see if she really can stand up to Utsuho.
She does the same thing in FMW3, though the setting is changed to the Palace of Earth Spirits. She also gets pretty damn bitter by the end of the fight, since drama.
Where the original Orin just directed the protagonist to Stage 6, in FMW she explains the entire situation to the party and Satori. It's all a part of Satori's terrible day.
SA Stage 6
Orin fights the protagonist one last time in Stage 6, because... I don't really know? Maybe she was worried they were too strong for Utsuho or something. Anyway the protagonist runs into Utsuho, who is nuts and plans to invade the surface. The protagonist obviously isn't very happy with this, so she kicks Utsuho's ass.
Aside from the exclusion of the Orin fight, Stage 6 is faithfully reproduced in FMW3. By the end, things look like they'll end peacefully like in SA. Then Shiro comes in.
Subterranean Animism has eight endings, two bad and six good. Most of the good endings have the protagonist figure out Moriya Shrine was behind the incident, so they decide to head over there.
Since Kanako and Suwako come clean in FMW3, none of the SA endings happen.
The protagonist storms Moriya Shrine again and beats up Sanae,
then runs into Koishi, who came to see if she could get a god for one of her pets too. She recognizes the protagonist from her sister's recollection of the incident, and challenges them to a fight. She loses, and it's noted in Koishi's profile that this was a good encounter for Koishi since it made her interested in other people again.
FMW replaces SA Extra with Chapter 55, which is basically an entire chapter about how SA could have gone horribly wrong. Koishi is left for the next game, where she'll presumably get a suitably dramatic conclusion.
Everything would have turned out fine if Orin had just gone to Satori in the first place, but she thought it would be better if she tried to hide what Utsuho was doing. If Satori had found out about Utsuho's plan, she thought, she'd waste no time dealing with Utsuho in a ruthless fashion. Of course, that wasn't true, but just as children are afraid of their parents finding out their secrets, Orin was afraid of Satori finding out about hers. Orin was somewhat in awe of Satori.
The last thing of note in the source game is the conclusion of Orin's character profile. Satori is much more caring in FMW so obviously Orin isn't worried about that, so instead the game makes it a plot point that the Palace of Earth Spirits crew are kind of bad at communicating.
Subterranean Animism leaves it kind of vague what happens next, but later appearances of Utsuho reveal she gained control of her powers and now manages a nuclear reactor.
...Satori Komeiji, if there anything we can do to help, don't be afraid to let us know.
I'm sure knowing how to properly handle a god would be helpful.
FMW provides an in-between phase and has the Moriyas step up and take responsibility for their actions.
Overall, FMW3 did a pretty good job with its SA adaption considering it only had five chapters to work with. Cramming two bosses into each stage was a good way to incorporate SA's reputation as a puzzle shooter of sorts, and the finale is grand enough the fact that the prior few chapters were kind of rushed doesn't really register. The game's writing has basically improved with each arc, so here's hoping FMW4 keeps that up for UFO and PoFV!
Actually, speaking of UFO, you know the geyser that set SA off? In the source games, it's what frees the Palanquin Ship and starts UFO. Like I said, all of the games following MoF are more interconnected.