| Summary
| - Bradley easily finishes off Greed and his comrades chimeras. When some of their spilled blood touches Alphonse, he suddenly recalls memories from when he was taken inside the gate in his failed attempt at reviving his mother. Back at Central, Barry the Chopper attacks one of Roy's soldiers, Riza Hawkeye. He fails, but subsequently makes a deal with the military. Bradley takes Greed to the homunculi's creator, "Father", who executes him for betrayal and absorbs the Philosopher's Stone inside his body. The Elric brothers return to Rush Valley to get Edward's automail fixed again. While there, they run into a prince of the Xing country, Lin Yao, who is also trying to find the Philosopher's Stone.
- While Edward is on study leave at South Headquarters for his annual assessment, Alphonse receives a note from a group of chimeras, claiming that they have important information about him. Alphonse tries to force them to reveal this information, but is captured and brought to the Devil's Nest bar where he meets another homunculus, Greed. Izumi and Edward both attempt to get Alphonse back, but are thwarted when Greed changes the composition of his body to resist damage. A military force under the nation's leader, Führer King Bradley, storms the Devil's Nest while Edward is fighting Greed in his hardened form, causing the battle to end prematurely. It is revealed that Bradley is actually the homunculus Wrath, and he proceeds to attack Greed before he can harden his body.
- Major General Armstrong meets with Bradley and takes Raven's seat in Central. Hawkeye gives Mustang a coded message that reveals Pride's true identity. Meanwhile, Father dreams about his first meeting with Hohenheim. It turns out that Hohenheim was infused with a Philosopher's Stone created by Father by destroying Cselkcess while Father created a copy of Hohenheim's body for himself. When Kimblee learns of the Elrics' actions, he faces Ed, leaving him seriously injured in the process. He is then rescued by Kimblee's chimeras, Darius and Heinkel, who had been betrayed by their boss. Al travels with Scar, Winry and May, but his soul starts trying to escape from his armor. Kimblee leads a battalion of Drachma forces against Briggs, while Hohenheim arrives in Lior and encounters Pride in an underground tunnel, declaring he will fight Father.
- Izumi and her husband Sig come to the aid of the Armstrong siblings and the Central soldiers to fight Sloth and manage to kill him. Back in Father's base, Hohenheim confronts Father alone, forcing him to return to his shadow-like form. King Bradley reappears in Central to fight all people against Father, but Greed decides to help them. Despite joining forces with the resistance, Greed is unable to hurt Bradley until Captain Buccaneer and Fu sacrifice their lives to wound him. Meanwhile, one of Father's subordinates activates a transmutation circle encompassing all of Central that absorbs Ed, Al, and Izumi.
- In Central, Riza discovers that Bradley's son is actually the homunculus Pride, who threatens her to maintain it in secret. In the north, Kimblee presents Winry as a hostage to ensure the Elrics' cooperation. He orders Edward to capture Scar, find Marcoh, and kill a large number of people from Briggs to help in the creation of a Philosopher's Stone. Kimblee's chimera soldiers, Jelso and Zanpano, are able to find and attack Scar. However, the Elrics come to the aide of Scar and defeat the chimeras to keep their actions in secret from Kimblee. Ed and Al capture Scar, but Winry asks for his help to fake a kidnapping so that Kimblee would not be able to use her as a hostage. While Scar escapes with Winry, May, Marcoh, and several soldiers to Briggs, Olivier is summoned to Central. Since another group of soldiers allied with Bradley come to Briggs, Alphonse goes to tell Scar's group to hide in another place.
- On their way to Dublith, the Elric brothers and Winry Rockbell stop in a town called Rush Valley, which specializes in mechanic automail. After helping a woman to give birth, Winry decides to stay in Rush Valley as an apprentice under her new friend's father. The Elric brothers go on to Dublith where they meet their old alchemy teacher, Izumi Curtis. The brothers are forced to reveal that Edward has become a State Alchemist, which is disliked by Izumi. As they tell her what happened, it is seen that Edward and Alphonse's father, Van Hohenheim left them when they were very young along with their mother, Trisha, who died a few years later. In an effort to bring her back to life, the brothers met Izumi and requested that she become their teacher.
- Edward returns to his hometown and meets his long absent father, Hohenheim. After a brief discussion, Hohenheim leaves before he suspects about the body Edward and Alphonse created. As such, Edward digs up the now buried body and discovers that he tried to revive an unknown person who was not his mother. As he returns to central, Edward reunites with Al and investigates what caused Al to lose his memories. The brothers then decide to fight against Scar to see if the homunculi will appear during the battle, thus bringing them closer knowledge on the Philosopher's Stone. The Elric brothers succeed in attracting Scar, and start fighting against him. Lin and his bodyguard, Lan Fan, decide to help them, and attempt to capture Gluttony, but Bradley discovers them and injures Lan Fan.
- Edward, Alphonse, and Winry return to Central, where the Elric brothers intend to do more research on the Philosopher's Stone and its whereabouts. Meanwhile, Second Lieutenant Maria Ross is charged with the murder of Maes Hughes as the real assassin, the homunculus Envy, was transformed into Maria prior to killing Hughes. When the brothers learn of Hughes' murder and Maria Ross' arrest, they hurry to confirm that the information is true. They encounter Barry, who has broken Maria Ross out of prison, but they are discovered by Mustang, who apparently kills Ross. To avoid any rumors about them, the homunculi Lust, Gluttony, and Envy go to attack Mustang and his soldiers.
- Barry starts chasing his old body after Lust orders it to attack him, triggering a battle consisting of Alphonse, Barry, Lin's men, and Mustang's crew against the homunculi. During the battle, Lust critically wounds Jean Havoc, one of Mustang's subordinates, paralyzing him below the waist. Mustang successfully kills Lust by repeatedly setting her on fire until her Philosopher's Stone is depleted. Lin and his men manage to hold off Envy and Gluttony, but they later leave under the order of a mysterious homunculus, Pride. Meanwhile, Edward is taken by Major Armstrong to the ruins of Xerxes to find Maria Ross with Mustang, having faked her death. As Maria escapes to Xing, Edward meets a group of Ishbalans, who tell him the story of the death of Winry's parents, who were killed by Scar in a previous war.
- After a brief fight, Ed, Lin, and Envy are swallowed by Gluttony. While they are inside, Envy reveals that Gluttony is an imitation of the gate that appears during Human Transmutation. As Envy explains that it is impossible to escape, he transforms into his true form, a giant creature, that attacks Ed and Lin. Scar and May search for May's little panda who is with Al, while Al goes with Gluttony to meet Father. Mustang encounters Bradley, who explains that he was once a human, but when injected with the Philosopher's Stone, he was transformed into a homunculus. Ed informs Envy that they can escape by using his Philosopher's Stone. Shortly afterwards, he finds the ruins of a country destroyed by Father. Ed, Lin and Envy reappear outside Gluttony, who is along with Al and Father.
- Scar decides to rescue Marcoh from the homunculi, so that he can find out more about Xing. The brothers leave Central to follow May, Marcoh, Scar, and his slave Yoki as they go to the icy north to learn the secrets of Xing's alchemy. Kimblee is freed from prison by the military so that he may kill Scar and kidnap Marcoh. Using Alex Armstrong's advice, the brothers arrive at the fortress of Briggs and meet Major General Olivier Armstrong, who is Alex's older sister. Both brothers are forced to work in exchange for staying with Olivier. As they investigate the fortress' lower level, Ed and Al encounter the homunculus Sloth, who has been digging around Amestris.
- Two alchemist brothers, Edward and Alphonse Elric, are forced to deal with a corrupt religious leader from the city of Lior, who is using a mysterious red stone that imitates the power of the coveted Philosopher's Stone to create "miracles". As they look for the supposed Philosopher's Stone, it is revealed that they want to use it to regenerate the portions of their body that they lost while attempting to revive their dead mother. In the interim Edward has had to resort to using automail prosthetic limbs, and Alphonse's bodiless soul resides in a body of armor. Edward defeats the religious leader from Lior but discovers that the stone is a fake. Using his status as State Alchemist, Edward goes to several towns with his brother to get closer to a real Philosopher's Stone, but they always end up becoming side-tracked with aiding civilians with their troubles.
- Al and his group are attacked by Envy, but Marcoh destroys Envy's Philosopher's Stone directly by using alchemy, reducing him into a parasitic form. Envy is given to May to take home with her, but Envy instead convinces her to go back to Central. The rest of the group arrive at Lior, where Al meets his father, who tells him his past dealings with the Homunculus Father. Meanwhile, Greed finds and kills the Chimera Bido, who was a friend from the original Greed. Greed then discovers he lost his memories and is still the same homunculus. Enraged, Greed betrays the homunculi, attacking Bradley for killing his partners. Having taken control of his body for a short time, Lin goes to where Ed and chimeras Heinkel and Darius are. For this reason, Ed and the chimeras decide to join forces with Greed to defeat the homunculi.
- Working with his father, Alphonse allows himself to be captured by Pride in order to grab him so that Hohenheim can trap him in a cave where there is no light, and so, preventing Pride from using his shadows. As Alphonse remains trapped with Pride, Edward, Hohenheim, Scar, Lan Fan, Jelso, Zanpano, and Darius join together to defeat Father, while Greed goes by himself. In Central Mustang reunites with his most trusted soldiers and kidnaps Bradley's wife in an attempt to defeat Father as well as the Military. Edward's group, May and Envy enter Father's base, but Hohenheim and Lan Fan separate from them. Edward's group and May are attacked by puppets injected with Philosopher's Stones, and Envy takes this opportunity to steal a body and recover his powers. Meanwhile, Kimblee finds Pride and Alphonse, and frees them after attacking Heinkel. Before falling unconscious, Heinkel gives Al a Philosopher's Stone to face Kimblee and Pride.
- After Ed defeats the guardians, the homunculi quickly incapacitate him when his arm fails to function correctly. They proceed to destroy Laboratory 5, cutting short the fight between Alphonse and the guard, Barry the Chopper. In the aftermath of the battle, Winry arrives in Central to fix Edward's arm. Meanwhile, Alphonse begins to suspect that he was simply created by Edward and that he is not a natural human. As he attempts to confront Edward about that, Winry shows up and tells him that he is wrong. The Elric brothers decide to head to Dublith for their next lead. After discovering a terrifying secret about some of the military's recent actions, Mustang's friend Lieutenant Colonel Maes Hughes is killed by the homunculus Envy before he is able to tell Mustang, who becomes determined to find the ones responsible for Hughes's death.
- Roy Mustang, a superior of Edward, directs the Elrics to meet with Shou Tucker, a State Alchemist who can teach them more about alchemy. Instead, they only discover that Tucker has turned his daughter into a creature called a chimera. As they leave, Tucker and his daughter are killed by a well-known assassin of State Alchemists known as "Scar". Furious about the extinction of his Ishbalan race by State Alchemists, Scar attacks the Elrics. Mustang and his soldiers come to their aide and save them, but Edward's arm and Alphonse's armor are damaged and they must return to their hometown of Resembool to receive medical and mechanical attention, accompanied by fellow alchemist Alex Louis Armstrong. They become sidetracked when they accidentally run into Dr. Tim Marcoh, a former State Alchemist who worked as a doctor during the Ishbalan War.
- Father heals the Elric brothers, as he sees that they are Hohenheim's sons and that they are important to him. He then uses Lin's body to host Greed's Philosopher's Stone, turning him into the new homunculus Greed. Ed and Al try to save him, but they are attacked by Envy and Gluttony. Scar and May arrive, but they are unable to fight the homunculi. Scar escapes, but Father takes both brothers and May to Bradley. By threatening to kill Winry, Bradley orders Ed to keep working for the State Military. As they return to the city, Ed discovers that all of Mustang's subordinates have been reassigned. Meanwhile, Alphonse meets with Lan Fan and May, who are being treated by Doctor Knox. Scar finds Tim Marcoh, who has been kidnapped by the homunculi, and orders Marcoh to tell him what happened during the Ishbal war.
- In Central, several soldiers, including Mustang and his subordinates, prepare to defeat Father by first attacking Bradley in a train. Edward meets Hohenheim again, and this time Hohenheim tells him his story with Father. Meanwhile, Pride kidnaps Alphonse and takes control of his armor using his ability to control shadows to attack Edward's group along with Gluttony. However, they are stopped by Lin's bodyguards, Fu, and Lan Fan, who has replaced her lost arm with an automail. Edward's group is then able to overpower Pride, who eventually loses control of Al. As a result, Pride eats Gluttony to absorb his Philosopher's Stone, and becomes stronger.
- Ed meets up with Hawkeye, who was assigned to be Bradley's secretary in the military, and she informs Ed of the events of the Ishbal war and how the State Alchemists were sent to kill the resistance: Mustang met with Hawkeye, and it is revealed that her deceased father was Mustang's teacher. Both Mustang and Hawkeye went to participate in the Ishbalan war along with Armstrong and Hughes. After several attacks, the Isbalans surrender and ask for help. King Bradley, however, orders the military to kill them off. As Scar and many other Ishbalans escape, they are attacked by State Alchemist Solf J. Kimblee, who kills most of them. Scar's brother transmutates his arm to Scar after gaining alchemical abilities, but dies. As Scar is being healed by Winry's parents, he panics after seeing his arm and kills the doctors. Once the war is finished, Scar escapes, and Mustang becomes furious at Bradley's behavior.
- Lin manages to escape with Lan Fan from Bradley, but they are followed by Gluttony. Winry becomes involved in the battle between the Elrics and Scar and learns about the latter killing her parents. However, Ed calms her down and he continues fighting Scar. Lin captures Gluttony, but Lan Fan loses an arm while helping him. A friend of Scar's from Xing, May Chang, saves Scar from the Elrics and escapes. Edward and his friends escape to Doctor Knox's house as they learn that Bradley is one of the homunculi. While they are healing, Gluttony loses his composure upon learning that Mustang killed Lust and attacks them. Ed, Al, and Lin help Mustang to escape by confonting Gluttony, but they are suddenly ambushed by Envy.
- Al uses the Philosopher's Stone to fight Kimblee and Pride. He eventually gives it to Dr. Marcoh who heals Heinkel, allowing him to bite Kimblee's neck through a surprise attack. After Al, Heinkel and Marcoh escape with help from Yoki, Pride decides to absorb the dying Kimblee. In Central, Olivier is attacked by Sloth and soldiers working for Father, but is aided by her brother. Ed's gang encounters Envy and May as well as Hawkeye and Mustang, who easily defeats the attacking puppets. Envy reveals himself as Hughes's murderer, causing Mustang to lose control and incinerate him until he returns to his parasitic form. Before Mustang kills Envy, Scar, Ed and Hawkeye convince him not to let his desire for revenge control him. Jealous with the humans' way to put aside their differences, Envy commits suicide. Back in Central, the soldiers ally with the Armstrong siblings to fight Sloth, but only Alex is able to continue holding off Sloth. At the same time, the Briggs soldiers manage to break into Central HQ, with help from Izumi.
- After being wounded by Buccaneer, Bradley is furiously attacked by Lin and falls into the moat. In order to honor Buccaneer for his sacrifice, Lin and Greed decide to join forces with the resistance to stop Father's subordinates. Meanwhile in Father's base, one of his men cuts Hawkeye's neck to persuade Mustang to perform Human Transmutation. However, the chimeras and May intervene and help Mustang heal Hawkeye. Seeing that Mustang will not perform Human Transmutation, Bradley and Pride ambush Mustang to force him to use it against his will, causing him to lose his eyesight in the process. Due to the transmutation circle that moved Ed, Izumi to the place where Father and Hohenheim are, Al manages to find his real body in the gate of alchemy, but refuses to recover it now as it has become so weak that it would not help him fight the homunculi. Therefore, Al reappears in his armor alongside Ed, Mustang, Izumi, Hohenheim and Father.
- The Elrics, along with the soldiers of Briggs, fight Sloth and manage to freeze him. Ed and Al tell Olivier all about the homunculi and ask for her help to protect the hostages they have secretly taken. They then discover that Sloth has been digging a tunnel around Amestris so that Father can transmutate the entire country. Meanwhile, Kimblee searches for and battles Scar. Kimblee is defeated, but is healed by a doctor with a Philosopher's Stone. After recovering, he meets with General Raven who has also been sent to Briggs to talk with Olivier. General Raven arrives at Briggs and asks Olivier to join the homunculi, but she kills him, instead. When Bradley discovers that the Elric brothers have asked for help, he orders Kimblee to take Winry to Briggs and force Ed to work for him.
- Thanks to their friend Winry Rockbell, an automail expert from Resembool, the Elrics recover from their battle with Scar. Afterwards, they head to Central City with Major Armstrong to find Dr. Marcoh's notebooks that reside in the First Branch Library. Upon their arrival, they discover the library has been burnt to the ground after a fight between Scar and artificial humans known as homunculi. Fortunately, they are able to recover a copy of Marcoh's notes from Sheska, a former librarian. However, the brothers are shocked to discover that the Philosopher's Stone is made by sacrificing human lives. They move through Central City to infiltrate an abandoned facility known only as "Laboratory 5". There they find that alchemical experiments were conduced using human sacrifices from a nearby prison. While investigating the lab, the Elrics are separated and forced to fight a pair of guards who have their souls sealed in armors like Alphonse.
- A flashback to the Elric brothers' younger days reveals the severe training they underwent as Izumi's apprentices. One such feat involved surviving on an island for one month while they fought Izumi's friend disguised as a wild animal. When they returned to Resembool, they attempted the failed resurrection of their dead mother. As a result, the brothers were forced into a mysterious gate that contained all the information of the world, but the payment for this information was the loss of their bodies. After recovering from that experience, they met Roy Mustang, and Edward took the State Alchemy Exam, becoming the Fullmetal Alchemist. Back in the present, Edward and Izumi try to think of a way to recover Alphonse's lost childhood memories, while Mustang prepares to be transferred to Central from Eastern Headquarters.
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