Al's blood seal lies just below the base of the neck at the back of the suit, on the inside. It is drawn with Ed's blood. According to Edward, he needs to be careful whenever he reconstructs Alphonse's body because he must keep the blood seal intact during the transmutation. If the blood seal is removed, Al's soul will be lost.
Alphonse is born in a small town named Resembool, where he lives with his older brother, Edward, and both of his parents, Trisha Elric and Hohenheim, until Hohenheim embarks on a journey and several years after, Trisha falls ill and dies, leaving the two young boys as orphans. Their neighbour, Pinako Rockbell, then begins looking after them. During that time, the brothers concentrate in studying alchemy in hopes of bringing their mother back to life and are able to train with a skilled alchemist named Izumi Curtis. When they return home from their training, they proceed to try the taboo art of Human transmutation but fail costing Edward his left leg, and costs Alphonse his entire body. Edward then performs a second transmutation, sacrificing his own right arm to bind Alphonse's soul to a nearby suit of armor.
In the manga Al eventually develops the ability to perform alchemy without a transmutation circle, the same as Ed. In the manga, when King Bradley impales Martel while she is inside Al's armored body, her blood spills onto his blood seal. This gives him a near-death experience, recalling to his mind his experience at the Doors of Truth. He realizes that he can transmute without a transmutation circle shortly thereafter. Also, in the manga, Alphonse is afraid that his armor will eventually reject his soul, which would mean his death.
When Ed was escaping from Gluttony's body, after being swallowed, the theory that Al's body was still in existence is proved, as Ed finds it on a return trip to the Doors, malnourished and unkempt, but very much alive. He shows the true nature of his body, showing that even though his body is almost impossible to recover, he won't give up, and so neither should they. During Ed's near-death experience, Al is shown as blacking out and seeing his body in the midst of a snowstorm. This suggests that his body is calling for his soul, showing the first sign of rejection. However, he manages to find the party and warns them, though Scar said that it is rather useless, since they had nowhere else to go.
Al is attacked by Pride and Gluttony, and was knocked out and possessed by Pride. However, with Ed's quick thinking and flash bangs, Pride's control over Al was broken. He then returned to the slum camp, where he met Hohenheim. Al came up with an idea to "beat" Pride. By Hohenheim using himself as a decoy, Pride moved all his shadows near him and was attacked by Al. Further distracted by Al, Hohenheim sealed Pride and Al in a large sphere made out of Earth. Al would be fine in there as he required no oxygen to survive. He started talking with Pride about how human he could be. At some point later Pride began banging on Alphonse's helmet, which Alphonse believed was just playing, but was really in order to send a Morse code through the earth to Father. This worked and Kimblee came and released Pride.
At this point, Kimblee and Pride proceed to ambush the group, and end up severely injuring Heinkel. Heinkel gives Alphonse the older Philosopher's Stone which was happened upon in the Briggs Mine. This gives them a great advantage, and with some strategical deception Heinkel is able to come back and deliver a fatal bite to Kimblee in the neck. Soon afterwards, the first stage of the giant transmutation circle is activated, and Alphonse is transported to the underground complex where Father is but when Ed calls to him he doesn't respond inferring that something happened while Al was transported there e.g. his soul might have separated from his armor body on the way there.
It is revealed that he was at the gate with his body, when he was about to get it back though, he goes back through the gate to help his friends, as his body was not suitable for fighting. After he leaves, his body states he would be proud to be his container, but mentions that his return to the other side may only bring despair and ruin. Alphonse returns to an overjoyed Father, since now all five sacrifices are here. He later prepares to battle Father along side his brother in the final battle, where he is powered by all the souls he had taken from Xerxes. One of his blasts severely injures Al as he tries to protect May Chang, damaging his blood seal.
When Ed's automail arm gets destroyed and he becomes close to being killed by Father, Al makes the decision to use May's alkahestry to perform the opposite of what Ed did for him, trading his soul for Ed's human arm so he can fight back. He returns to the other side of the gate where he reunites with his body, waiting for Ed to come get him. Ed later trades his ability to use alchemy to restore Al's body, giving up the ability to use alchemy forever. After readjusting to his original body, Al journeys to the East to learn more about alkhestry so that he and Edward can pool their knowledge and help everyone they met during their journeys, including the getting the surviving human chimeras back their humanity. A later photograph shows that he and May remain together in the future.