All the Fullmetal Alchemist stuff I've been reading/writing lately has made me come to a realization. Alchemist view their discipline as a science. It involves extremely complex mathematical equations they have to do in their head. The biggest effects involve detailed circles. Then it hit me:
Fullmetal Alchemist/Magical Lyrical Nanoha.
Two ways I can see this playing out: Either you have the whole Jewel Seed thing happen in Amestris instead of Japan, which means that Nanoha never appears but you still get most of the supporting cast. While the idea of Ed ending up with Raising Heart is funny, it more likely that Al (being the lover of all things cute, furry, small and pathetic) would rescue Yuno. Magical Giant Armor Suit Alphonse! (It's even more like Gundam now!) Of course, the Homonculi are likely to notice the Jewel Seeds and start trying to snap them up. We know the Homonculi can eat philosopher's stones to greatly increase their personal power, so what's to say they can't do the same thing to a Jewel Seed or ten? And then Precia finds out about human alchemy, specifically the part that allows you to bring back the souls of the dead and attach them to a handy vessel...
The second way would be to have a more true crossover, using the first anime continuity. In that setting the use of Alchemy could register as an interdimensional scale threat (what with it eating the souls of people from across the dimensional void) with the Philosopher's Stone acting as Lost Logia. Mustang, when he was using an incomplete Stone in the first anime could annihilate entire cities all by himself (as in the "snap his fingers, entire city lights on fire" scale). So while having the later season Nanoha cast showing up in the manga continuity would probably be a curbstomp, in the first anime it would be easier to level the playing field. (Not to mention that Hohenheim by himself is basically Green Lantern, and the Homonculi are more powerful in the first anime as well.)
In either continuity I could easily imagine Ed freaking out about magic at first, but once summon sat down and started explaning the mechanics of it, in which case he'd probably accept it as just a really advanced version of alchemy and take to it like a fish to water.
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Epsilon
Fullmetal Alchemist/Magical Lyrical Nanoha.
Two ways I can see this playing out: Either you have the whole Jewel Seed thing happen in Amestris instead of Japan, which means that Nanoha never appears but you still get most of the supporting cast. While the idea of Ed ending up with Raising Heart is funny, it more likely that Al (being the lover of all things cute, furry, small and pathetic) would rescue Yuno. Magical Giant Armor Suit Alphonse! (It's even more like Gundam now!) Of course, the Homonculi are likely to notice the Jewel Seeds and start trying to snap them up. We know the Homonculi can eat philosopher's stones to greatly increase their personal power, so what's to say they can't do the same thing to a Jewel Seed or ten? And then Precia finds out about human alchemy, specifically the part that allows you to bring back the souls of the dead and attach them to a handy vessel...
The second way would be to have a more true crossover, using the first anime continuity. In that setting the use of Alchemy could register as an interdimensional scale threat (what with it eating the souls of people from across the dimensional void) with the Philosopher's Stone acting as Lost Logia. Mustang, when he was using an incomplete Stone in the first anime could annihilate entire cities all by himself (as in the "snap his fingers, entire city lights on fire" scale). So while having the later season Nanoha cast showing up in the manga continuity would probably be a curbstomp, in the first anime it would be easier to level the playing field. (Not to mention that Hohenheim by himself is basically Green Lantern, and the Homonculi are more powerful in the first anime as well.)
In either continuity I could easily imagine Ed freaking out about magic at first, but once summon sat down and started explaning the mechanics of it, in which case he'd probably accept it as just a really advanced version of alchemy and take to it like a fish to water.
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Epsilon