Confusion ..

Since Alphonse is a scientist, it is only normal that he would question his existence if he drop his feelings in the matter and just think it out logically. Meeting a hollow suit of armor like him who is a smartass talks as if he understands Alphonse's body better than anyone else, ticked Alphonse off and confused what he believes in.

What if your personality and memories were all fabricated by your big brother?

→ Barry the Chopper, Fullmetal Alchemist vol. 4

Of course Alphonse trust his older brother Edward with his life however, Alphonse still fears his existence at first when he was doubted by the thought of fabrication. It started when the Elric brothers learned that the *Laboratory Number 5 might be a secret laboratory for making Philosopher's stone, the Elric brothers sneak there to investigate. Alphonse was left outside the building by Edward because he couldn't fit the ventilation. Alphonse fought a soul bound armor like him and also who was an ex-mass murderer named Barry the Chopper.

Alphonse Elric Alphonse Elric Alphonse Elric Alphonse Elric

Barry told Alphonse that there is a possibility that Edward just created him as a toy and his existence and memories where all fake. Although Alphonse is intelligent enough to not believe all the crap Barry was saying, but Alphonse remembered that his older brother once told him that Edward has been hiding something from him and was to afraid to mention. This triggered Alphonse to question his existence. The thing that his older brother might be hiding is the fact that his existence were all fake.

What am I suppose to believe with this empty shell of a body!!!? According to alchemical theory human beings are composed of physical body, mind, and soul. Memories are nothing but data if you think about it. ... Maybe what you want to tell me was that my soul and my memories where all fake and they were created artificially.

→ Alphonse Elric, Fullmetal Alchemist vol. 4

Well from this, it is true that he could question his existence if he is just a soul without knowing where his body is. I've already explained where Alphonse's original body is and how it is connected and still living. But on this point of the story, they don't know about that possibility yet so I'm sorry for spoiling that to you early. haha.

*Winry (Ed and Al's childhood friend) smacked Alphonse and told him to go after his older brother who left the room after Alphonse mentioned about his "fabricated" existence. Winry told Alphonse that no one in their right mind would sacrifice his life just to create a fake brother. Winry told Alphonse that the thing that Edward has been afraid to told Alphonse was the fact that whether Alphonse blames Edward for what had happened to them. Knowing that he made a huge mistake, Alphonse run towards Edward and made up.

I think that somewhere inside Alphonse, he is still bothered by the fact that he is an armor and is sensitive with the matter. But who wouldn't?? He is finding and searching for a way to bring back his original body that the possibility to succeed is 1 in a million. At this point of the story, he doesn't know where to find their answer on what they are searching for, and they just lost the possibility of achieving it through the use of a philosopher's stone knowing that creating a stone means murdering people. Alphonse could only move forward because Edward never gives up on him. In this point of the story, Alphonse is like a lost boy in the forest searching his way home.

Vocabulary *Philosopher's Stone is a powerful red liquid that could over pass the law of alchemy which is made up of human souls.
*Laboratory number 5 is one of the 5 laboratories given by the government for their scientist and state alchemist to conduct research.
*Barry the Chopper is a mass murderer who chops off girls and his wife for entertainment. He was supposedly sentenced to death, but his body and soul were seperated from each other secretly and is used as a guard for Lab #5 as Number 66.
*Winry Rockbell is Edward and Alphonse Elric's childhood friend. She is also Edward's personal automail mechanic.