Current Story Ideas in idea page.
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Grand Order/Fate/Percy Jackson
Shirou from Sword Order is summoned into a singularity that occurs in the Percy Jackson setting using Greek/Roman heroes. (It's essentially a fleshed out event quest)
Vinland Saga/Fate
Arthur Proto in Vinland Saga, the return of the one true king
Arknights/Fate
Asclepius or Shirou as the Doctor that can cure Originium infection. He wakes up as a parallel version of himself known as the 'Doctor.'
Yu Yu Hakusho/High School DXD
Yusuke is summoned by King Yemma after his stint as a demon king because the Yokai Faction seeked his help.
Fate/Warhammer Fantasy
Shirou is reborn in the Fantasy setting. His powers naturally attract the attention of multiple factions, who want him under their thumb or dead for their own reasons.
Fate/Nier: Automata
Idealism and magic meets existential dread and technology.
Basis could have the Fate world itself crossing over into this one or vice versa. Otherwise Shirou is simply flung into this not-so-perfect future, either sometime after establishing himself in stay/night or during one of the routes while still trying to determine who he is and the hero he wants to be.
Fate/Fire Emblem Awakening
Kaleid: Shirou would initially be against fighting another world's war, but would inevitably be drawn into it despite his best efforts. His motivation would be to reunite with the sister that was not sent to the same world. This Shirou is far more competent due to having to fight a grail war with no allies.
Fate/UBW/HF: Shirou. He would be gung-ho about the war effort should the possible end be revealed to him. Perhaps initially decides to defend a village. Maybe befriends a future Shepherd and joins that way. Introduced to the FE world via dead apostle hunt.
Fate/Kara no Kyoukai (Garden of Sinners)
Fate and Shirou crosses over with other Type Moon works such as Witch of the Holy Night or Kara no Kyoukai. This leads to varying interactions among cast members. The interactions between Shirou and Ryougi Shiki would be golden. One who lost his identity and strives to save everyone, valuing the lives of others, meets another with perhaps an identity too many to express, viewing the value of death. Their ideals and attitudes on life will lead to disagreements between the two protagonists, potentially building to armed conflict, especially given who they are and the choices they make. Though it is possible for them to come to an understanding.
Tokyo Ghoul x fate
Shirou is the summon and task to raising Eto before the events of Tokyo Ghoul and how Shirou beliefs clash in that World. Also Shirou willing gives portion of his body to prevent needles killing.
Fate x Seven Deadly Sins
Shirou, preferably (but ultimately up to you) a UBW or Kaleid, ends up in the world of the 7DS, finding himself in front of the Boar’s Hat. He has no idea what’s going on in the world he’s arrived in, but Meliodas is nice, and so long he works as the cook for the place, the blond doesn’t have a problem giving him a place to stay, since being at a roaming bar is sure to get him plenty of information.
He accepts, and he works with Meliodas, and learns more about just where he’s ended up over the next few weeks, but still without an idea for how he got there… Or possibly “why”... Then, a few more days pass by… And Elizabeth shows up.
Fate/Danmachi
Shirou has developed an odd relationship with the legendary Zelretch, who apparently has taken an interest in his desire to reach Artoria again, so he provides him with “help” in the form of vague information, coordinates to places where he could find artifacts, old thaumaturgical knowledge he could actually use, and occasionally dumping him into other worlds.
Once again Shirou finds he’s been unceremoniously dropped into a new World, one where gods walk the Earth, giving Mortals blessings to become adventurers. Shirou finds himself drawn to a down on their luck Familia of two, Hestia and her first and only child, Bell Cranel. A letter from the Wizard Marshal informs him that this trip is going to take “a while longer than usual.” and “Don’t be afraid to call up some company.” And thus, the nameless Wandering Hero arrives in Orario.
TLDR: Post Fate Shirou winds up in Orario because Zelretch is bored, and thinks he’ll shake up the world’s order. He maybe summons some servants for Hestia and later maybe some allied Familia. Artoria shows up because Shirou/Artoria.
Fate/Tales of Series
This suggestion is under the assumption you have played any of the Tales of Series.
Shirou, from any of his routes, ends up in one of the Tales of Series (Symphonia, Zesteria, Graces, Arise, etc.) parties’ midway through their journey and becomes a close companion of the protagonists. I imagine this story being more of a way to explore Shirou’s philosophy post any of his visual novel routes and how having true companions helps him grow as a person and have a slightly healthier look on life.
(I've played Arise, and saw the Tales of Abyss anime- Parcasious)
Fate/Worm
UBW Shirou in Brockton either at the beginning of canon or around the time Leviathan is attacking. I kinda want to see how Earth Bet reacts to a completely selfless hero. Not to mention how Cauldron would react to Zelretch.