A fan-made crossover game of Touhou and EarthBound/MOTHER, made in RPG Maker 2000 by 'S'.The game begins when a Meteor crashes into Gensokyo. After Reimu and Marisa fight of the mysterious alien that arrived with it, they find an unconscious boy nearby, who reveals that he has no memories. Soon after, things go to hell in Gensokyo. Not that that stops the lightheartedness and endless references to other works.The translated game can be found here, while a playthrough can be found here. A sequel to the game, Return of Touhou Mother, is currently being uploaded as a series of videos by vgperson here.
This game contains examples of:
Amnesiac Dissonance: When he first arrives, Porky has no memory of his past. Unfortunately, he gets better, and later fakes his amnesia to further his plans.
A really jarring one happens in the sequel: You'll have spent a lengthy part of the game playing as Ness, right up to freeing Reimu of her mind control, at which point she attacks you out of anger - and then you're suddenly controlling Reimu and fighting against Ness.
Darker and Edgier: While the first game has a large number of lighthearted and comical moments in the middle of everything, Gensokyo's industrialization and the human/youkai conflict it escalates are always taken quite seriously. The sequel takes a pretty hard hit of Cerebus Syndrome as well, to the point where you have to squint for any humour that isn't in the battles.
Demoted to Extra: While the gameplay leans decidedly towards the MOTHER side of things, the characters from said series are for the most part pushed to the wayside - even Lucas and Claus are mere side characters. There's a reason for this.
Not so on the sequel though, where Ness enters the scene proper as a playable and important character.
The Dragon: Tenshi works against the heroes more than almost anyone else, effortlessly beats down Remilia and Yukari, and unlike the other Touhou characters is never persuaded to switch sides until the very end of the game, after Porky turns her into a robot to cover his escape.
Fake-Out Fade-Out: Both times against Tenshi's final attack. The first time has Ridley's battle music, the second time has Bhava Agra As Seen Through A Child's Mind start back up at full force.
Fantastic Racism: One of the conflicts for the sequel, found near the end of Chapter 1. Porky was just the nudge needed for the humans and youkai to realize just how much they disliked each other.
Glass Cannon: Marisa, having the second-highest speed and IQ, along with two immensely potent spells, but with the lowest Defense and HP.
Gods Need Prayer Badly: Source of a fairly bigMood Whiplash in the sequel. En route to your next destination you happen upon Sanae and a very transparent Kanako. They explain that the incidents in the previous game caused a great many humans to no longer believe in or care about gods, so Kanako's physical being is vanishing from the world. And then when you return to that area later, neither Kanako nor Sanae are present.
Grey and Gray Morality: Are the humans justified in liberating themselves from the youkai they had feared for so long by merging Gensokyo with the Outside World? Or is it the youkai who are justified in keeping the humans under their thumb if it means preserving Gensokyo?
In a surprising twist, the sequel reveals that MOTHER 3 (in this continuity anyway) chronologically precedes the Mother series and thus this fanseries; it's made apparent by the Absolutely Safe Capsule making an appearance and Porky returning near the end. There may be a chance that this trope will finally be averted...
Know When to Fold 'Em: After Reimu throws off Yukari's helmet, the latter pretty much just leaves the scene rather than force it back on.
More than Mind Control: In the sequel, it's assumed that Yukari put a mind control helmet on Reimu. It turns out that Reimu put it on herself, after Yukari told her what it did, because she was so distraught by everything that was happening and didn't want to think anymore. Yeesh...
Murder the Hypotenuse: Marisa wants to be the one to save Reimu so badly that she's willing to kill Ness just so he can't.
Mundane Made Awesome: JoJo's Bizarre Adventure-related items are presented with much more dramatic fanfare than the normal items. How much? Finding Remilia's full JJBA collection causes the earthquake in the Scarlet Mansion.
Marisa is fought twice in one of the later chapters in Return.
Rogue Protagonist: In the sequel. While Reimu doesn't qualify due to More than Mind Control, Marisa is a different story - she is absolutely livid at Ness, whom she holds responsible for her friend's current state.
Stable Time Loop: The game's author seems to have gone with the "MOTHER 3 precedes EarthBound chronologically" route, so all of the characters are living in the world Lucas rebuilt using the Dragon in Mother 3 - which Porky was born in. Loose knowledge of those two games is all you need to know what happens next...
The Revolution Will Not Be Civilized: The humans who want to rebel against the youkai's rule aren't portrayed in a positive light. After all, they are led by Porky and if they get what they want, Gensokyo will vanish as the consequence.
Time Skip: The sequel is set six months after the end of Touhou Mother. Things aren't going well.
Took a Level in Badass: Cirno goes from goofy comic relief boss battle to one of the more difficult boss battles in the game sometime while the party is stuck in Old Gensokyo.