Fate stay night in shirou's place probably. Nanites will heal sakura when they first meet as kids, i will also figure something to save illya(maybe have kiritsugu ask to be turned evo in his last days to save her?), they will both live with mc as adopted sisters (is this tecnicaly kidnapping? Maybe. Will they mind? Hell no!). I think illya will be rescued when mc is arround 6, followed by kiritsugu's death a few days later, and sakura will be rescued at her and mc's age 8 (so before the worst stuff start with her (if you know you know :( )), i will also make some excuse for mc to be the one to find and rescue medea near the start of the war instead of that emotionless dude i forgot the name of (probably picking flowers in the woods with illya or something)
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About mc's magical affinities, his element will be "nano machine" and he will decide not to learn of his origin affinity
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For the servants, sakura is still getting rider medusa and illya is still getting berserker heracles, medea and heracles already get along well, and medusa will bond with medea over their similar pasts. I am unsure if mc will still get saber artoria or not(probably will), i also have to decide who medea will bind with (if anyone at all (nanite bs for the win)), and i also have no clue what to do with the assassin servant spot (maybe have medea summon hassan of serenity for some reason, and have mc use some nanites bs to make her poison an active ability instead of passive( on top of beeing immune himself alongside his family again, due to nanites bs))(maybe having medea summon jack the reaper so she can finaly have a home where she is loved?). All friendly servants will stay on earth after the war ends due to (you guessed it) nanite bs (if van kleiss can make a time machine with this tech, i don't see how making a mana generator to keep the servants runing would be a stretch!)
So we have 1berserker, 2saber, 3rider, 4caster, 5assassin on mc's team, rin will also likely colaborate so 6archer shirou is also on board as mc is not shirou himself. Poor lancer cu, maybe i should have mc rescue him from the master he hates instead of forcing him to 1-VS-all the war, lol. So with 7lancer on mc's team, all servants are on mc's side, all antagonists that are left are kirei and gilgamesh(shinji would have died a day after the matou patriarch(who died when mc killed the bugs on sakura), once the mages learned that the matou had no competent magic users left, they invaded the matou estate and stole EVERYTHING, a "gas leak" beeing the explanation to the public on how the house just vanished)... should i go with apocrypha rules and get another set of 7 servants summoned maybe? Or maybe have them go to chaldea?