soul binding ...

When the Elric brothers committed Human Transmutation when they where young in order to resurrect their mother, Alphonse lost his entire body as a *toll. At that time of the incident, Alphonse's soul entered the unknown creature that they transmuted or "created".

Alphonse Elric Alphonse Elric Alphonse Elric

Before Alphonse was able to remember his experience in the *gate of truth, they thought that it was their mother who again died in that incident. Alphonse was able to remember his experience inside the gate of truth when he wasn't able to protect a chimera who manipulated his armor while they where in Dublith under Greed. The chimera was killed by King Bradley while she was inside Alphonse. Right after her death, Alphonse remembered his lost memories of the gate of truth and was unconscious until Edward woke him up. Alphonse was able to remember the time where he was reaching out to his brother. It was Alphonse who was inside the creature that they "created". It was never a human being.

The Process:

Alphonse Elric It is said that binding a soul inside an armor takes a lot of knowledge needed. Edward was merely 11 years old when he bounded Alphonse's soul inside an armor which came from his father's collection. Edward was bleeding from loosing his left leg when he bounded Alphonse soul and lost his right arm as a toll. It wasn't mentioned how the specific process is, but the soul and the armor is bounded by a rune or a blood seal. The only person who can restore Alphonse's armor from getting scratches from their horrendous battles to its original state is Edward. Edward is the only one who has the knowledge to restore his armor.

It is also said that a human person consist of body, soul, and mind. Alphonse has a theory after meeting Barry the Chopper ( an ex-murderer who's soul is also bounded in an armor ) that there will be a time when his armored body would reject his soul because they are not compatible together. He might look like he is immortal from people who are looking for immortality like Greed and Ling because Alphonse doesn't have the need to eat, sleep, or get hurt, but to Alphonse he feels like he is like a "ticking bomb".

Living Body:

Alphonse Elric Alphonse Elric Alphonse Elric

So where is Alphonse's original body? It's not rotting away like Alphonse feared his body would, but because he and his older brother's soul interwined when they commited the Human Transmutation, Edward has been giving nutrients to Alphonse's original body by constantly sleeping and eating a lot. Alphonse's body still exist inside the portal of truth where it sat in front of his own gate waiting for his soul to get him. You might ask how is his body able to move around and think without a soul? Every alchemist has their own "truth". In Alphonse's case it's his Truth who took his own body. His body can think for itself and act like Alphonse because he has Alphonse's brain and it is moving because of *Truth, its simple as that.

Vocabulary *A toll is something that is the most important thing that alchemist has. For Alphonse, warmth and the feeling of kindness from the people that he loves is something that he cares about, which is why his body was taken so that he would never feel again.
*Gate of Truth is the door that separates the Portal of Truth (a white place/space where the Truth resides) and their world from each other. The gate of truth also contains memories and alchemy knowledge.
*Truth is an unknown white creature who gives judgements to alchemist who tries to overuse their alchemy and try to overpass God.
*A chimera is a single creature that contains two distinct cells.
*Dublith is a city of Amestris where Alphonse's teacher Izumi Curtis lives.
*Greed is one of the homonculus/enemy.
*King Bradley is the Fuhrer of Amestris.
*Human Transmutation is an alchemical and forbidden act that would resurrect the dead.