When the sacrifices are forcibly summoned in the room with Father, Alphonse's soul isn't present. In the white room, Alphonse claims that he wants his body back but refuses to do so saying "I can't fight in a body like this". This seems to imply that he could have gotten his body back at that point and returned to the real world with his soul back in his human body. But if this were the case, Izumi and Edward would have just opted to get whatever they were missing back. Since in the show, they don't get their respective body parts back, the scene with Alphonse and his physical body doesn't make much sense. Anyone care to explain?
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I don't think so. If he had taken his body back right then, he still would have been stuck in the gate. It took Ed's sacrifice to "balance the books" and get Al's body and soul back from Truth. As for why Al refused to rejoin his body and soul right then with the logic of "I need this armor body right now and can't fight with my real one", I think it was more along the lines of him not knowing at the time that he, by himself, couldn't return to the real world with his real body.
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I hope I'm making sense here lol.
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From what I’ve been able to rationalize it is due too that when some thing dies. All it means is their “souls vessel” is broken. The body breaks down and becomes part of “the whole”. While that is happening The soul goes where ever it does. (Recycled into another body? Transferred into another type of energy? Who knows where souls really go.) Thats the normal cycle at least.
Human Transmutation fails for somewhat of a good reasons
A soul brought back from death, can not exist perfectly within a vessel that is not its original. (Berry the choppers soul was ripped from his vessel somewhat damaging it, and put said soul in a suit of armor. The armor doesn’t decay, or weaken. But the spongy body that was left behind, had a animals soul placed inside of it. So the body started to react and decay.)
You don’t always call back the correct soul. (And therefore, the created vessel from the transmutation doesn’t look like it is suppose too.)
When Ed and Al did their HT they tried to call their mother’s soul back. (which they did not). And the result was a horror show. The trade in their transmutation was Al’s entire body and soul. And Ed’s Leg.
Note, I said it was traded. Not destroyed. Broken down sure, but it’s parts were very much still on the other side of the gate. (They use this concept in FMA 2003, which is why wrath has eds arm and leg). (This must have been a bit of influence from arakawa).
Ed then trades his arm for al’s soul and bonds it to a piece of armor. (Leaving the “intact” body beyond the gate).
Now We dont see Barry the choppers soul getting “called back” like Al’s because his vessel already has a soul in it. But Al’s vessel is perfectly fine, however it is soulless.
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During the ending scenes alphonse does sort of toy with the idea of having his body back, but he would be stuck in it. He wouldn’t be able to “fight” because he would still be “traded”. He’d be gone. Back where it started so to speak.