Heh. Nice to see people attempt a Persona 3 fic. After playing the game, I'm all for fics that, change things here and there. Like not have the same ending as the game (which, while I won't spoil it... or not. I mean, um, isn't this thread basically full of spoilers? Kind of has to if you want suggestions.
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I see most of the points either have been made, or ones that I haven't thought about, but does make sense. There are a lot of issues for Minato if he desires to 'change' his (and the world's) future.
I'm still not sure why he shouldn't be leader. I mean yeah, being a part of SEES itself could be a burden to, helping stop The Fall. At least early one, he would be watched carefully. But as someone else noted, he did seem to have a lot of freedom. Meeting a kid, karaoke, drinking coffee, he did seem to have a lot of freedom. Now, you could argue that he was being watched anyways (who knows how powerful Ikutsuki really was), but at least on the surface (if you choose not to go that deep), he had plenty of places put whatever plan Minato has in motion. Of course there are 'problems' when coming up with a plan, mentioned before, and mentioned (repeated?) in the following thoughts.
While we now know that stopping the 12 shadows is the wrong thing to do, at least early one, it's not wise to let them 'live' either. After all, what about all those Apathy Syndrome cases? And as mentioned before, the first moon boss you encounter, if you let that one live, Minato, Yukari, Junpei, and the unknowing transmogrified passengers would be dead. While capture is one idea, problem is, you'll have to convince the others that you should capture, and not kill. And of course, the main issue to that would be Ikutsuki. Even if Minato knows he's a bastard, the others won't hold the same belief until presented with hard evidence that he can't be trusted.
The evidence part is where it gets tricky, and yeah, been touched on before as 'how can Minato get evidence'? First, what can Minato do? Break into the Chairman's room? Not going to happen if the dorm is as 'wired' as we think it is. Second, the Chairman had, for the most part, built a perfect... 'persona' as a behind the scenes leader, researcher, and overall go to guy for SEES. Until the "ZOMG PLOT TWIZTZZZ!!!!" scene, no one would have suspected he wanted the world to end, instead of trying to save it. The only way Minato could prevent this would be, either make Ikutsuki as someone not to be trusted, or, somehow bring doubt about Ikutsuki's true intentions.
Going to Jin or Aigis was suggested. There are problems with both ideas. Though I could think of a way Jin could be 'contacted' with you could say. Aigis, the main problem is that Ikutsuki pretty much has control over here. Until her 'emotional' side took over, there was nothing Aigis can do to stop him. Certainly not turn against him until it is too late. Not to mention, it'll be a while before Aigis becomes 'available' to help.
Jin? Well the issue is why would he trust a member of SEES, or even how Minato can contact him. One way, the revenge website. It might take some 'technical know how' for Minato to discover that Jin was a part of it, but it's not impossible. And this is where I think it would actually be beneficial for Minato to be leader of SEES. Early on, Strega simply followed them and tried to assess if they are a threat or not. What if, Minato, as 'leader' of SEES, contacted them first, gave them the reason why SEES is doing what they are doing. And, being leader, has doubts. Instead of simply going 'we should capture the 12 shadows, instead of destroy them', he could go 'you want to save the Dark Hour? I do too. However, just because I'm 'leader' doesn't mean I can do everything. I can't stop them from replacing me or killing them unless...' and this is where Minato could get Jin to help them uncover the truth about the 12 shadows.
Of course this has other issues too. Like, if Jin finds out the truth, will Jin continue to work with Minato? Or turn against him and actually encourage them to kill the 12? Could be an interesting avenue to explore.
Another idea brought up, if he simply went "Hey! I'm from the future and this happened...", well, besides that fact that if Ikutsuki found out, he'd have him killed, it would also, as mentioned before, potentially alienate him from his dorm mates. Yeah, they could believe in him (especially if he tells them stuff only they would know), but that won't make them friends with them. I mean, just imagine if someone from the future went back and told your life story. Besides wondering how they knew (immediately bringing up privacy issues) trust issues are also brought up. I mean, as far as they know, he's just a stranger. A stranger that knows too much. Is he using that info to really benefit the future? Or is he using it for nefarious reasons? Information can be bad in the wrong the hands. Besides, part of the idea is that this fic would have a happier ending right? Preferably with one of the girls right?
I'm sure they are more issues that need to be dealt with. But I'll leave them for someone else to talk about, or, until I finish the game.
I spoiled myself with the ending. But I haven't finished the game yet either.