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 episodes 3 to 9, when the brothers had performed 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 brothers become very close to Tucker's young daughter, Nina, who views them as her older brothers, calling Edward 'little bigger brother', which the usually height-sensitive Ed accepts. During this time, Ed, Al and Nina are invited to Maes Hughes' home for Ed's birthday and Maes' wife Gracia goes into labor that same evening, Ed discovers his ability to use Alchemy without a Transmutation circle when he inadvertently heats water to comfort Gracia. Edward passes the State Alchemy exam by saving another candidate during the practical test using alchemy without a circle. Soon after, Edward writes to Winry and in doing so, inspires Nina to write to her mother. When Ed finds Nina's letter incinerated, he becomes suspicious and after expressing his suspicions to Maes, he 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. During this time, a serial killer is terrorizing the city and when Ed accompanies Hughes to the scene of the killer's latest crime, Ed is reminded of his mother and his failed attempt to alchemically resurrect her and faints. By the time Ed comes round, he is back at Tucker's home but he and Alphonse are then forcibly removed by Basque Grand as a result of Ed investigating Tucker's research.
Ed and Al return to confront Tucker and subdue the guards outside. By this time, Tucker 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' and is tempted to try and split them up but they are already fused to the core so he is forced to back down rather than cause further harm. 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 apologises for being unable to save Nina and starts to mourn. To Ed's chagrin, he is tasked with gathering up Shou Tucker's research as Tucker has apparently been executed. Ed vows to catch Nina's killer.
Soon after, Winry is kidnapped by the serial killer whom 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 removes Ed's automail arm. He is found by Al and, while crying, says he had never been so terrified in his life as he thought Barry was going to kill him as well as continuing to lament their failure to save Nina.
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 once again encountered 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. This encounter with Scar left Ed with his automail arm destroyed and Al having to be carried in a crate and when they were preparing to travel back to Resembool for repairs under Armstrong's watch, Maes Hughes informed Ed that Scar killed Nina.
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 has become a monstrous chimera himself and has been attempting 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 and battles with Scar, finally confronting him for killing Nina. 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. Later, Ed finds Al, who is now the Philosopher's Stone, thanks to Scar, who died after he sacrificed his two arms.
Afterwards the Elrics are now fugitives from the military and escape to Resembool with Ed intending to desecrate his mother's grave to gain a part of Trisha Elric's remains to use against Sloth. Though the Mustang Unit catches up, the Elrics explain to Mustang what Martel told Al before she was killed which is that King Bradley is a Homunculus. He learns from Winry that his father is in Resembool, and is still angry with him, before Hohenheim disappears before the following morning, followed by the Mustang Unit leaving shortly afterwards, with Mustang needing to draw the other search teams away and confirm if Ed is telling the truth. However, Ed also learns from Sheska shortly after Mustang's departure that Hughes had died for apparently knowing too much.
After leaving Resembool, the Elrics face against Lust, Sloth, and Wrath, with Lust joining their side, and because Al is hesitant to use their mother's remains against Sloth, this gives Wrath the opportunity to absorb them into his body. Eventually Al is able to come around and after killing Lust elsewhere, Wrath returns and his determination to protect Sloth by merging with her exposes Sloth to Trisha's remains allowing Ed to finish her off once and for all. After Envy kidnaps Al and Izumi arrives and drives off Wrath before could attack Ed, the two head to Central Command hoping to find the Führer for a lead on the location of Al's whereabouts. Despite not going as planned, the Tringham brothers who were arrested for impersonation the Elric's again before Maria Ross and Denny Brosh freed them provide Ed a clue they found from their father's notes. While Izumi stays behind to fight the new cybernetic Frank Archer, the Tringham brother's lead Ed to the location of the Homunculi's hideout.
Ed discovers that Dante faked her death at the hands of Greed and use the Philosopher's Stone to transfer her soul to Lyra's body. Edward also learns Dante's past with Hohenheim 400 years ago. Edward then was informed by Dante in Lyra's body that she is next to transfer her soul to Rose's body. Dante uses Rose's baby to open the Gate and Ed is sent to the other side of the Gate. When he awakes he finds himself in another body that looks almost exactly the same as his. He sees Hohenheim, who confirms Ed's suspicions that he is in fact in another world. It is revealed that Ed and Hohenheim are in London during World War I. Hohenheim explains that the huge amount of death in this world is the source of all alchemy in their world, he also tells Ed that only his soul and mind crossed through the Gate and that his body is still inside, making it possible to return using his inner Gate.
As Dante opens the Gate in order to take Edward's arm and leg from Wrath, Ed re-enters his own world. Ed and Envy engage in a fight, Envy changing from form to form, including Tim Marcoh, Mustang, Maes Hughes and others, trying to take Ed off guard. Ed demands to see his true face and Envy reveals his true appearance, which holds a resemblance to Hohenheim. Dante tells him that Envy was the first Homunculi created when Hohenheim tried to bring his and Dante's son back to life, over four hundred years ago when he died from Mercury poisoning. Using this news as a distraction, Envy transforms his arm into a blade and stabs Ed through the heart, killing him. Al breaks free before Gluttony can completely devour him and plans to revive Ed, because his soul is still at the gate and has not yet crossed over. Envy tries to stop him, which ends with Envy meeting Edward at the Gate. Envy learns that Hohenheim is still alive on the other side of the Gate and sets out to kill Hohenheim, against Ed's advice.
When he wakes up, Ed learns from Rose of Al's sacrifice. After having Rose leave and take Wrath, Ed uses an array, with the same technique he used to bind Al to the suit of armor, in hopes of bringing Al's soul back from the Gate. Flashing ahead to the epilogue, it shows Edward in London, preparing to leave for Germany. He explains to Hohenheim that there is a rocket scientist in Munich who he believes may be able to help him get home. As Ed is on the train, he vows to someday be reunited with Al.Noah, Ed finds himself embroiled in a conspiracy by the Thule Society, bent on invading his own home world.
But before that, he meets Hohenheim, now partially consumed by Envy, again in the Thule Society as he finally tells Ed and Al that he is sorry for everything. His father sacrifices himself alongside Envy to open the Gate and once again send Edward home. Reunited with Alphonse and Winry at last, and joined even by Sheska, he is equipped with new automail, and, with the aid of Alphonse, manages to defeat the Thule society. However, Edward had to cross the portal again to close it from the other side, bidding a goodbye to both his brother Al and Roy Mustang. Afterwards, Ed finds Noah cradling the dead body of Alfons before realizing that Alphonse had managed to hide himself in a suit of armor almost identical to the one he was trapped in the anime. After Alfons' funeral, Ed and Al decide to locate and dismantle Alfons' atomic bomb.