This is likely going to be the last Toaru idea I post for awhile, as recently I've posted several of them in succession. This may also be the last time I post for quite awhile on this collection, considering how long it took me to work out the specifics of just this idea.
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So I was thinking that maybe, rather than just science and magic, we say that there's a spiritual side, too. We then have to choose whether or not Imagine Breaker is able to negate spiritual entities. For the sake of things being easier, it's probably best if Imagine Breaker can only negate hollows, as well as maybe things like the Hogyoku, though the Hogyoku shouldn't be involved in this fan fiction anyway.
That doesn't mean it should have no effect on other spiritual entities, though. If a shinigami has a gigai or a human body, they should be sent back into it via touch of Imagine Breaker, and if the spiritual entity has no human body or gigai, they should be temporarily immobilized. I'm not sure what it should do to quincies or fullbringers, but as for Visoreds and Arrancars, they should be able to be purified into shinigami, but only if Touma wills it. This is so that Ichigo doesn't lose his hollow abilities just because he touched Imagine Breaker. I'm basically saying that unless the visored or arrancars state that they want to become regular shinigami, Touma won't purify them, because that's how Touma is personality-wise and all. Hopefully that makes some amount of sense.
Then comes the question of whether Imagine Breaker purifies hollows or destroys them like quincies. I think it's best if you have it so that it destroys hollows if Touma wants them to be destroyed, and purifies them if he only focuses on negating the hollow energy. I know Imagine Breaker doesn't typically work that way, but has there ever really been a situation where it's needed to work that way? I think it's okay to have a little bit of leeway there.
Have it so that Soul Society and the other spiritual powers know of the magic and the science sides, and so that the magic side knows of the spiritual side, but that they don't really interact with each other outside of spiritual items being used by magicians. Soul Society will interfere when necessary, however, and so Ichigo is sent by them to find the secrets behind Aleister Crowley just in case of disaster.
Also, have Soul Society not know of who Touma is, nor that he has Imagine Breaker, but be aware of his actions throughout the magical side of things. I want this to become a plot point later on, where Soul Society, or at least the royal guard, come and tell Ichigo about how they have long known of the existence of Imagine Breaker and it's capabilities, since it was once feared among all the residents of soul society, but it was long thought to have been lost to time.
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With the technicalities out of the way, I will now get into why Ichigo arrives in Academy city, and who he interacts with during the story. I want this story to take place shortly after TYBW, but not directly afterwards, maybe a couple months later or something, and I also want Kisuke to accompany Ichigo to help gather data on espers. I want the idea to be that Ichigo has been ordered by Soul Society to find out why Aleister Crowley created espers, and what he intends to use them for, but they get dragged into all of the problems in the city instead.
This can take place anytime during the canon of "A Certain Magical Index", but I'd prefer it be as far into canon as possible, though there are limits to how far you can go due to Crowley being one of the main focuses. Have it so that everyone in Academy city can see shinigami, and that there are no hollows around the city.
I don't know how Ichigo will be able to disguise his powers as an esper ability, but maybe he can just outright say his spiritual energy is his power. Just say that he has control over all things spiritual, uses his swords to help channel that power, and that if he uses too much it temporarily corrupts him, thus the semi-hollow-like appearance every now and then. He should also be labeled a newest level 5. It's not the best explanation, (to the cast of the series) for his strength, but it's the best one I could think of, even though the system scan should not realistically work on any spiritual abilities. Ichigo should always be in his spiritual body throughout the story, unless forcibly pushed back in by Imagine Breaker, though I don't know how you'll explain his shinigami attire.
Touma-wise, have him meet Ichigo somehow, and then have them become semi-friends that bond throughout the various happenings in Academy city. I can't really say anymore in that regard, since I'm not focusing on a particular point in canon, but have him interact with all of the various residents of Academy city and all. I think it would be particularly interesting to see him and post last order Accelerator interact, seeing as they actually have a lot of similarities, when you really think about it. They're both protecting something, and they're both doing it in order to repent for something; in Ichigo's case a little less so, but I'm mainly referring to his mother's death, and how he feels it's his fault and all. Maybe a better way to put it would be that they both have a desire to protect following self-inflicted tragedies.