The year is 1905. As young Roy Mustang stands, decked out in his new military uniform, in his alchemical mentor’s home laboratory, the master of the house informs his protégé that he is not ready to learn Flame Alchemy and that it would be pointless to teach even the basics of alchemy to someone , who would lower himself to a military dog. Roy argues that alchemy is to be used in the service of the people and that the state military is the organization best equipped to offer this service to those in need, but the ailing master angrily rejects this excuse. Lamenting his master’s poverty, the young Mustang explains that state certification would lift him out of the misery of this dilapidated mansion and even allow him to complete his research, but the old man explains that he completed his research a long time ago – research into the most widespread possibly powerful and destructive form of alchemy. Lamenting that his life as an alchemist is over, as his research ends, the master succumbs to a coughing fit and collapses to the floor. Roy panics and rushes to his teacher’s aid, his cry of concern reveals that his mentor’s last name is Hawkeye. Master Hawkeye whispers a request for Mustang to take care of his young daughter, explaining that she is the only one who keeps a record of his completed work.
A few days later, just after the Master’s funeral, Roy stands in front of his grave with a young Riza, who thanks Mustang for helping with the funeral preparations. He gives her his contact information and encourages her to contact him in the military if she ever needs anything. When asked if she too will judge him for donning the uniform, Roy mentions that his dream is to become part of the foundations of the country and protect its people with his own power, but Riza replies that it’s a wonderful dream and hopes for one day. when they will all live happily ever after and wonders if Roy is the right person to make his father’s dreams come true.
In the present, Lt. Hawkeye is taking a shower in his apartment, and as the water runs down her back, over a large and ornate tattoo half covered by large burn scars, she hears Black Hayate barking at the front door. When she gets out of the shower and checks the noise, she finds that Edward Elric has stopped by for a visit and invites him inside. Ed explains that he heard about Hawkeye’s questionable reassignment, returns the lieutenant’s gun, which he immediately begins to clean. Ed then explains to her everything that has happened since they last met – including the incident with Scar and Winry. Ed laments his inability to stick to guns and blames himself for being so naive when even though Winry cried over her parents, his and Al’s deaths caused her more pain. Hawkeye urges Ed to hold on to this feeling so he can survive for the sake of those who care for him, and advises him to protect Winry if he loves her that much – to which Ed responds with an embarrassed denial. Riza then apologizes for adding to his burden by giving him the gun, and Ed responds by asking her if the gun ever felt like a heavy burden. Riza replies that the fact that she has taken so many lives of her own accord means that she no longer has the right to complain about it as a burden, and, understanding that he means the lives of the Ishvalans, asks if she can tell him what happened during the Ishval Civil War.
In the Homunculi’s underground lair, Scar demands that Marcoh tell him exactly what the Amestrians did in Ishval during the war.
The year is 1901. The people living in the harsh, unforgiving desert land of Ishval are relatively unhappy with the recent annexation of their homeland by the larger nation of Amestris, but are able to keep their upset in check until an American soldier accidentally shoots and kills an Ishvalan child. Tension turns to rage, and the rage fuels a series of disturbances that become war—a war that spreads like a plague through the eastern region of Amestris and continues for seven years.
The year is 1908. Tired of the endless battles in the East, Führer King Bradley signs Executive Order No. 3066, calling the State Alchemists to battle on the front lines. Riza Hawkeye, a young sniper in a war zone, considers that the death of enemies is absolute only when facing snipers or state alchemists. Iron Blood Alchemist Basque Grand, Strong Arm Alchemist Alex Louis Armstrong, Frost Alchemist Isaac McDougal, Silver Alchemist Giolio Comanche, Crimson Lotus Alchemist Solf J. Kimblee, and Flame Alchemist Roy Mustang wreak untold havoc in Ishval, destroying dozens of rebels despite some having doubts , whether their actions are justified. As the wounded Comanche is being dragged from the field, young Captain Maes Hughes recognizes his old military schoolmate Roy in the camp and strikes up a conversation with him. However, each of them can see that the other’s eyes are clouded by the lives they have had to take. They go for a walk and lament that their youthful ideals have been overwritten by the horrible future they helped create. When they question how on earth Ishval could justify such a gross military expenditure, they are approached by Cadet Hawkeye, who Roy is horrified to see has also obtained the eyes of an assassin.
At the camp, Hawkeye asks Mustang why the soldiers are murdering their fellow citizens instead of protecting them, and why alchemy is used to kill people to serve the people. Nearby Solf J. Kimblee, overhearing the conversation, haughtily replies that it is, because using alchemy as a weapon falls within the job description of a state alchemist, and killing people falls within the job description of a soldier. Roy gets angry at Kimblee’s remark, but the Crimson Lotus Alchemist explains that it’s people like Mustang and Hawkeye that he doesn’t understand. He asks them if they donned their military uniforms and entered the battlefield without realizing that they would be called upon to kill. A call to action comes and Kimblee leaves for his next mission, but when Hughes does the same, Roy stops him and asks his friend why he continues to fight. Maes simply replies that he fights because he doesn’t want to be killed, adding that while the reason may be simple, people’s reasons for acting are always just as simple.
Back in the present, Marcoh explains to Scar that one of the reasons for the war was the development of the Philosopher’s Stone. Several Ishvalan POWs were brought to Laboratory 5 in Central City, where a five-point transmutation circle was used to extract their souls and condense them into a single stone. Enraged, Scar demands to know what happened to the Philosopher’s Stone, and Maroch replies that it was given to Solf J. Kimblee. Recognizing the name, Scar remembers Kimblee’s attack on his family and the death of his brother.
The year is 1908. As Solf Kimblee single-handedly decimates vast areas of Ishval with the Philosopher’s Stone, the tide of the entire war is shifting. Logue Lowe, a high cleric of the Ishvalan religion, surrenders to Führer Bradley in exchange for the lives of all his surviving compatriots, but Bradley flatly rejects the deal, noting that Lowe’s life is worth only one life and cannot be compared to dozens. thousands of remaining Ishvalans. Lowe’s followers cry out that God will punish Bradley for his wickedness, but the Führer replies that God is only a concept created by men, and that if one wishes punishment after another, they must enact it with their own hands instead of relying on a deity.
The war is finally coming to an end, and as the soldiers prepare to be shipped home, Hughes and Mustang express their newfound disillusionment with the military. However, Mustang hopes that the system can be changed and longs to complete his original dream of protecting the citizens with his own power, shielding those below him and urging those below him to protect those below him. Some time later, after Roy is placed in a command position at the Eastern Region Headquarters, he is approached by Riza Hawkeye, who remained in the military after the war, and asks to be placed under him. After hearing that he plans to bear the suffering of others so that a future without suffering can be created, Mustang appoints Riza as his aide and bodyguard and authorizes her to shoot him if he ever strays from the right path.
In the present, Edward claims that even if Mustang becomes Führer, the nation will not change as long as it remains a military state; Hawkeye explains that the Colonel plans to appoint a national assembly with greater democratic power and seek to prosecute war criminals like himself. Ed is shocked to hear that Roy is taking such a potentially self-destructive path, but Riza states that it is their duty and penance for what they have done. He switches and urges Ed to return Al and himself to their original form to bring happiness to the people who care about them.
Alphonse prepares to leave Dr. Knox’s house and says goodbye to May, who thanks him for all his help. When Al properly introduces himself, May realizes that the Fullmetal Alchemist is his older brother and suggests that they are of the same temperament; Al takes offense, describing himself as a much more dignified person than his brother and insisting that his human body is prettier than Ed’s. Hearing this, May’s affections shifted rather sharply from the older Elric to the younger.
Under Envy’s central command, he brings fresh food to Marcoh’s room, but when he enters, he finds the doctor’s broken and headless body lying on the floor, his blood painting the word “Vengeance” across the wall.