When he started this quest, with Alphonse coming along, Edward did in fact fear something.
Not of being ordered around. Who would when you are becoming a state alchemist, those who are called the 'dogs of the military'? He highly disliked this, because he knew there is a dark side to everything, and this was partly the reason he refused to have Al be one too.
Not of Al leaving the journey and going back to Resembool. Sure he would be lonely, but Alphonse would be much safer back home. Although, Al is stubborn and would come along no matter what…
Not of the philosopher's stone being a mere myth. Somewhere in his heart Ed had a small voice denying the existence of the philosopher's stone, dooming Al to be a soul in armor forever. But when did he ever listen to anything other than his immature and stubborn voice?
No, Ed was afraid of losing his path. Of becoming apathic towards other humans. Of becoming cold and unfeeling. He was scared that on the road to restoring both Al's and his own bodies that he would do things that would cause not only Al, but Winry as well, to distance themselves from him. That he would sacrifice other lives to make his and Al's better. He knows this is what the military does, sacrifice others, sometimes a whole race, to make things easier for others. Sure Ed had a temper and a short complex, but he genuinely cared for others. If he actually used human lives for something, Ed wasn't sure if he would ever forgive himself.
Which is why when he found out what the Philosopher's Stone actually was he was disgusted. Why when he almost used it to save Al in the laboratory, he was so furious at himself even if he didn't show it.
This is a bit short, and I am not exactly happy with it.
So excuse this sad little piece?
~Tora ^^