So, after beginning my fanfiction, I realized I might as well add this in. This explains a little bit of what isn't explained well in the story. It gives you an idea of when during the story line this is and what differences there are. I'm sorry for the confusing set up. I did this from memory the first time and went back to fix it after watching the episode. Since I don't have time right now to rewrite the entire thing, I'll have to leave it for now.
If you want to just go watch the anime to explain it (because I'm really bad at it), episodes forty-one and forty-two should explain it all.
After hunting Scar to Liore, Ed finds out about the transmutation circle placed around the entire city. He tries to warn the military, but is eventually ignored. Meanwhile, Alphonse is turned into a time bomb by Kimbley (The Crimson Alchemist who specializes in exploding things). He is unable to move due to the chemical reaction. Before he is fully consumed by it, Scar transmutes his arm into Al's armor. By doing this he makes Alphonse the vessel for the philosopher's stone. He then activates the transmutation circle.
After all the citizens of Liore have been evacuated, Scar continues his plan. The military, at this time, has been led to believe that the people of Liore are planning an uprising and that they need to go in and stop them. This information is false, however, and Scar uses it for his plan. With the innocent citizens out of the way, Scar activates the transmutation circle just as the soldiers are sent into the city. These soldiers are turned into the Philosopher's stone which forms inside of Al's armor.
What I have changed from this story . . . Alphonse is consumed just as Scar activates the transmutation, so instead of being created inside of Al, the stone is just a normal Philosopher's stone. I have also changed the place that Al is laying. Instead of close to the center, surrounded by buildings, I have placed him towards the outside of the town, close enough to the edge to be seen by those outside the circle. Other than this, the changes are quite obvious.