The Alternative Tale
Edward and Alphonse Elric arrive at Reole, hearing about Father Cornello who can perform miracles and claims to bring the dead back to life. The Elric brothers set out to confront after him their meeting with Rose Thomas, a woman that is mourning her dead boyfriend Cain and the death of her parents when she was a young girl.
As the Elrics confront Cornello, they revealed their past about Ed losing his left leg and Al losing his entire body. With Ed's left leg gone, he sacrificed his right arm to bind the soul of Al to a giant suit of armor. A past of the Elrics' childhood is shown from episode 3 to 9, when the brothers had perform alchemy (Ed in age 6 and Al in age 5), their love with their mother, Trisha, the horrors that began when their mom died due to an illness. Even during the time, the sons of Trisha sends letters to their father Hohenheim, who never answers their letters. The horrors showed what happen to Ed and Al's bodies.
Afterwards, the Elrics met Lt. Colonel Roy Mustang who recruits the boys to become State-Alchemists of the State Military due to seeing the failed Human Transmutation. Mustang also stated that he received a letter from the boys, inquiring Hohenheim of course. Shortly then, Winry and her grandmother fit two automail limbs for Ed in place of his right arm and left leg. Edward and Alphonse then leave Resembool to travel to Central City.
Along the way, they met Majhal, whose name had appeared on their father's letters relating to Human Transmutation. Majhal had an elderly woman following while meeting with the Elrics, and the Elrics also met Claus, a young girl who reveals that her sister was killed by a zombie. Majhal revealed that he had a lover named Karin who died, and later the elderly women who followed him was actually Karin. Ed discovers that Karin lost her memories and has aged. Once Karin's memories have returned, Majhal fails to recognize her due to his passion of reviving her. Majhal then attempts to murder Ed using his sword, but in self-defense, Ed knocks the sword right out of his hand, which then flies into the air and impales Majhal through his stomach, killing him.
The Elrics then move on to Central City, but encountered a group of terrorists led by a man named Bald, then later defeats them with the help of as we all know, Roy Mustang's best friend, Maes Hughes. When they arrive in Central City, Mustang advises that they stay with an Alchemist named Shou Tucker, known as the Sewing Life Alchemist. Over the course of a few months that they stay and study at the Tucker home, both the brother's become very close to Tucker's young daughter, Nina, who views them as her older brothers. Al, Ed and Nina are invited to the Hughes' for Ed's birthday and pull together with great difficulty to help Maes' wife Gracia after she goes to labor during the proceedings. Edward passes the State Alchemy exam by saving another candidate during the practical test using alchemy without a circle. Soon after, Edward discovers that Tucker, who was famous for creating a talking Chimera, created the Chimera by transmuting his wife, who Nina believed to have left them two years earlier. By the time Ed arrives to confront Tucker, he has already transmuted Nina and the family dog, Alexander into another talking Chimera. Ed realizes that the Chimera is Nina when she calls him 'brother'. After the military become involved, Ed helps Nina/Alexander escape from custody but they are deconstructed alchemically by Scar. Ed soon discovers the deconstructed body of the Chimera. He vows to catch Nina's killer.
Soon after, Winry is kidnapped by a killer who has been terrorizing the city and someone Ed believes may have had something to do with Nina's death. Ed and the killer, who calls himself Barry the Chopper, fight after Barry removed Ed's automail arm. He is found by Al and, while crying, says he had never been so terrified in his life as when he thought Barry was going to kill him.
Ed agrees to search for the Philosopher's Stone in hopes of restoring his and Al's bodies. The brother's begin helping people as they continue the search, including the Tringham brothers (Russell and Fletcher) who had been chasing their father Nash's failed research regarding to the Philosopher's stone and later states to live their own lives thanks to Edward. Back to Central City, Ed reports to Mustang about his missions, and later challenges him to a duel in order to pass his yearly assessment and learn about Doctor Tim Marcoh, to which he and Al meet with Mustang's information, though unknown to them was killed by the Homunculus shortly after Marcoh passed off information to them to where they could find his research. It was also during this time with Marcoh whom Ed became acquainted with Scar to whom Ed realized he met 3 years ago in Central, and was nearly killed, but was saved by the Mustang Unit and Major Armstrong.
After learning from Marcoh's notes, Ed and Al head for the Fifth Laboratory. There, the Elrics, along with Scar, meet Lust, Gluttony and Envy as well as Shou Tucker, who became a monstrous chimera himself and in hopes tries to revive his daughter, Nina. Scar, also became aware of their relationship, and helped them escape.While recovering his wounds at the hospital, Ed tells Hughes about the homunculi and the other events in the 5th Lab which leads to Hughes' death in Episode 25 by Envy. Alphonse ran away due to Ed not telling him about if Al is really an artificial soul and what was Ed afraid to tell him. Ed meets Al again after Al ran into Scar and helps him with rescuing an Ishvalan child from a mercenary. Ed reluctantly lets Scar go with his people, but later decides to follow them down south suspecting Scar may not have told him everything about how to make a Philosopher's Stone. This journey south is interrupted when Ed, Al and Winry are dragged to Dublith by the Elric brother's alchemy teacher Izumi Curtis and her husband Sig. They meet a Homunculus by the name of Wrath, whom Ed discovers that it was Wrath he saw in the gate and took his right arm and left leg, giving the Homunculus the opportunity to perform alchemy. They also discover that Izumi's connection to Wrath is that her and Sig's baby died while a stillborn and Wrath was created when Izumi tried to revive her dead infant son through Human Transmutation, which Wrath admits he hates Izumi as well.
Afterwards, Wrath escapes and at Izumi and Sig's butcher shop, Izumi after disowning the Elrics as her students sends the Elrics to met Dante, Izumi's former teacher. While at Dante's mansion, they encounter her student, Lyra (who the Elrics met in episode 9), who wished to become a State Alchemist. While at the deep forest, Al is kidnapped by Greed and his chimeras.
This leads Ed into searching for Al. Ed then finds Al, Izumi, Sig and Greed and confronts Greed. Ed later goes on and kills Greed at Dante's mansion thinking that Greed was responsible for Dante's death, though Dante's body was on the floor and Greed had just arrived at the mansion. After defeating Greed Ed learns that when a Homunculus is exposed to the remains of the human they are modeled after it causes them to become weak, enabling them to be killed.
After a brief trip to the Southern slums and learning what from the Ishvalan Exile that there was no other way besides human sacrifice to create the Philosopher's Stone and that he explained this to Scar, before Scar left with the intent to create a Philosopher's Stone to thwart the oppressive actions of the State Military, Ed decides to hunt down Scar before he kills again. Ed parts ways with Winry; after Winry reluctantly takes his earlier advice about leaving their side for her own safety along with the fact she is now aware of who in the State Military killed her parents.
While traveling down to Ishval, Ed meets and forms and uneasy alliance with Martel, the only survivor of Greed's gang. When in Ishval, Martel informs the Elrics the harsh secret of the real cause of the Ishval Civil War. After meeting with Heymans Breda and Jean Havoc, Ed and Al upon traveling with them to the nearby Military Base learn that Scar has been spotted in Reole and is building a giant Transmutation Circle, likely to sacrifice Reole's population to create a Philosopher's Stone.
With Frank Archer's approval Ed heads into Reole alone to confront Scar and battles him. Their battle is interrupted by Lust and Gluttony before they are driven away thanks to the locket that Scar recovered in Ishval prior to his arrival in Reole. Lyra and Rose, the Holy Mother then appears and Lyra convinces Ed to hear Scar out first. Scar reveals his past to Ed and also tells of what the military did to Rose and the rest of Reole. Ed discovered that Scar real intent is to use Archer's troops as the ingredients for the Philosopher's Stone. So because of this, Ed helps Rose and the Reole citizens escape from this fate battling Wrath and Sloth in the process, confirming that Sloth is the creation from the Elric brother's working with Human Transmutation.
After a dying Solf J. Kimblee used alchemy to transform Al's armor into explosive material to get his revenge against Alphonse for previously humiliating him, Scar transferred all of his incomplete Philosopher's Stone into Al to save his life. As a result, Al became the Philosopher's Stone. Shortly after, Alphonse learns his body became lighter and his blood seal could endure contact with water. He also gained the ability to perform alchemy without a circle, although this is due to him "remembering" the gate. He only uses alchemy twice after he becomes the stone because any alchemy he or anyone near him uses activates the stone and destroys a part of Al's body. Because he houses the Stone in his body, he becomes the primary target of Dante's attempt to cheat death, but not before he becomes a pawn in Shou Tucker's plot to resurrect Nina. Once captured by the Homunculi for Dante, Al was to be devoured by Gluttony to complete the Stone inside Gluttony's body. But when he saw his brother killed by Envy, Al uses the stone's power to restore Edward's body (including his missing limbs) and re-bind his soul to it. This destroys his own body as he used up the whole of the Philosopher's Stone in the transmutations.
Alphonse becomes the Philosopher's Stone and regains full memory of his visit to the Gate. The concept of this is never fully ventured, due to his fear of the possible outcome effects of using the Stone's power. In the final episode of the series, he clearly uses alchemy without the need of any transmutation circle, in order to resurrect his dead brother. After Ed is revived, Ed performs one last transmutation on himself and sends himself to our world to pull Al's body and soul back to Amestris.
When Al came back to his body, he had forgotten his experiences in the armor and was physically the same age as when his body was taken away by the gate.
Alphonse is later seen back in Resembool playing with Den. Izumi and Sig come to Resembool to visit and while they are having dinner with Alphonse and the Rockbells, Alphonse asks Izumi if she can train him again so he can have further knowledge of alchemy. Izumi agrees to train him saying, "I can't say no to that face" and so Alphonse goes with Izumi back to her hometown of Dublith so they can train.
It is revealed in the movie, Conquer of Shamballa, that Izumi became ill and could not train Alphonse anymore so she told him to leave. She did not want Alphonse to see her dying because it would have been hard on him, so Alphonse returns to Resembool. But, Alphonse did not stay there for long, he left his town so he could travel the world.
In the Conqueror of Shamballa, Al has grown into a powerful alchemist. Two years have passed since the final episode of Fullmetal Alchemist. He is first seen walking in the desert, where he transmutes a well to drink water.
He eventually comes to Reole, just in time to save the town from the Thule Society's soldiers in armor suits. It is revealed that he still hasn't regained his memory of the past years, not recognizing Alex Louis Armstrong, however, he is determined to find his brother. As the suits of armor are sucked into the portal in the sky, Al manages to bind a part of his soul to one of them, having figured out that the portal leads to the parallel world where Edward is. Once the suit is on the other side, Al, who is able to see through it and control it, meets Ed, and is overjoyed to see him, but the two are forced to flee immediately as the Thule Society's troops start shooting. Eventually, after talking to Ed, Al's alchemy wears off, but not before he reassured Ed that they'll meet again. Later, Alphonse (with Wrath observing) prepares the circle to get the Gate open, but realizes that the sacrifice is needed. They are attacked by the powered-up Gluttony, who Wrath lures into the circle, letting him bite him and asking Al to open the Gate using both Homunculi as sacrifices. After the Gate opens, Thule Society begins their invasion of Amestris, and Al, having met up with Ed, sets out to fight its forces. With the help of Roy Mustang, they defeat Dietlinde Eckhart, however, Ed leaves to close the portal on the other side.
After crossing the portal, Ed finds out that Al had managed to hide himself in a suit of armor almost identical to the one his soul had been bound to. After Alfons' funeral, Ed and Al decide to find the atomic bomb and dismantle it.