During a festival from Resembool Hohenheim converses with a young Pinako, who asks him why he remains closed from all the villagers. In the same time, he faces a demon identical to him talks to him about the humans' weakness, as the story so far is recapped. In the end, Hohenheim finds encouragement from a young Trisha, and he wakes up to discover it was all a dream as a result of drinking too much alcohol.

Alphonse and Gluttony arrive at Father's lair, when Ed, Envy and Ling burst out of Gluttony's stomach. Alphonse, Edward and Lin then battle Father and the homunculi. Father then uses his strange powers and turns off Ed's and Al's alchemy, rendering them vulnerable. Lin is then captured and given the Philosopher's Stone, turning into Greed. Scar and Mei then arrive and engage in battle, during which Xao Mei reunites with Mei and Scar finds out about Envy's murder which triggered the Ishbalan Civil War. At the end of the battle, Gluttony dies and Father extracts his Philosopher's Stone.

Envy leads Ed and Al, who has sneaked May in his armor, out of Father's hideout, which is actually under military HQ, to meet with Bradley. Ed threatens to quit the military, but Bradley says he will kill Winry if he does. However, he allows Ed and Al to continue their research. Roy enquires if Bradley was the one who killed Hughes, which he wasn't. After checking Winry is alright, Ed and Al encounter Greed, who gives them a message to Lan Fan from Lin. Meeting up with Bradley, Greed points out that Lin is still fighting for control. Roy reveals Bradley's identity to Armstrong, and ponders that there may be another homunculus hidden in the shadows. Al passes on Lin's message to Lan Fan, as well as telling her about him and Greed, encouraging her to get an automail arm. Ed, hearing that other alchemists alchemy had failed the same time as his and Al's, wonders how Scar and May's alchemy works. Meanwhile, as Father creates a new copy of Gluttony, Scar encounters Marcoh in their prison, who begs him to kill him so the homunculus cannot use him for their plans. However, Scar demands to hear more about the Ishbalan war from him.

Years ago, Roy's desire to become a state alchemist is disapproved of by his teacher, Berthold Hawkeye, Riza's father. Before he died of an illness, he asks Roy to look after Riza, who has an alchemic symbol on her back. In the present, Ed visits Riza to return the gun she gave him and asks about Ishbal. After the war broke out, Bradley passed a document announcing the extermination of the Ishbalans. This takes it toll on many alchemists, including Roy which isn't helped by the taunts of Kimblee, who enjoys killing. As Marcoh tells Scar his side of the story, he reveals that he was involved in using Isbalans to make the Philosopher's Stone, which was given to the state alchemists to enhance their alchemy. The Ishbalan leader tried pleading with Bradley to end the killing in exchange for his life, but was rejected. When the war finally ended, Roy resolved that he would work to become the new Fuhrer to protect the people and appointed Riza as her second-in-command. Riza mentions to Ed that when they finally achieve peace, they may have to be punished for the people they have killed. When Envy checks Marcoh's cell, he finds nothing left but a beheaded corpse and the word "vengeance" written in blood on the wall.

Ed passes on what Riza told him to Al, and the two contemplate about what to do after they complete their objectives, and as to why Scar and May's alchemy worked when their's was blocked. However, May had run off, so they go and look for her. Meanwhile, Riza, Breda, Fuery and Halman say their goodbyes as they are sent to different HQs, with Roy finding a hidden message inside a chess set Halman gave him. Roy later reminds Ed that he owes him 520 cenz, but Ed decides to keep ahold of it until he becomes Fuhrer. Roy uses the note he got from Falman to make contact with Grumman. Meanwhile, Fu is shocked to find Lan Fan had lost her arm, and declines Ed's help to find an automail mechanic, since it would involve his acquaintances in their troubles. Afterwards, Knox gets a visit from his children, who are pleased to hear he's been able to successfully treat patients. Realising that Marcoh had escaped along with Scar, Envy releases Kimbley from prison, giving him to the task to retrieve Marcoh and kill Scar. Wanting to find out more about Kimbley and the secrets behind his brother's alchemy, Scar destroys Marcoh's face so it won't be recognised, before heading off to the North to recover his brother's notes.

As May heads off towards the North with one hooded person, Scar escapes with another to the West. General Grummon, disguised as a woman, meets up with Roy to discuss current matters. Upon hearing that Grumman saw May at the train station, Roy asks Armstrong to pass the message onto Ed, who had decided to look in the library for information on alkahestry. Upon passing on the message, Armstrong also gives Ed a letter of introduction to pass onto General Major Armstrong, his sister. Later on, Ed and Al meet Bradley's adopted son, Selim, and are invited to his house where they also meet Bradley's wife and are later joined by Bradley himself. After the meeting, Ed and Al head off towards the North. Meanwhile, Scar and his accomplice escape from the train heading West, and Kimblee tries to predict his next move.

Still on Scar’s trail, Kimblee figures out that he headed north and follows him there. When Kimblee gets word that Scar and Marcoh are on a train, he boards it by having another train run alongside it, but instead of finding Marcoh, he finds Yoki there. Kimblee is then attacked by Scar, and the two recognize each other from their previous encounter years ago. Before Kimblee can really do anything, Scar impales him with a metal pipe, and this leaves Kimblee no choice but to use his alchemy to separate the two parts of the train, with Scar on the other part. Realizing that something happened, the train’s operators stop it and find the injured Kimblee, but he orders them to keep going. Unbeknownst to Kimblee, the real Marcoh is heading north on foot with May Chang. The two eventually reach the shack where Scar’s brother’s research is located, and they find it intact.

Upon entering the fortress, Ed and Al are taken to the medical room where Ed is treated for frostbite. One of the workers reveal that the northern automail used by Buccaneer is made of aluminum and carbon, and Ed's normal steal automail does not work well in the cold. The brothers then are visited by Olivier who demands the brothers tell her about their intentions. The Elrics tell Olivier about their quest to get their bodies back and their search for May, but they don't talk about their dealings with the homunculi. Olivier knows that Elrics are hiding something from her, but she agrees to help search for May and also orders the brothers to go to work, since there's no food for the lazy.

After Olivier comes up with a plan to stop Sloth, Buccaneer forcefully recruits the Elrics and Falman for the plan. With everything in place, Olivier and her trio of tanks ram Sloth into the elevator which is sent down to the level with the exposed walkway. The confused Sloth walks out of the elevator and immediately gets fuel spilled onto him by Buccaneer's group and is pushed over the railings with a combined effort from Olivier's tank, Falman, and the Elrics. The fuel spilled onto Sloth is cold weather fuel that evaporates even in the middle of winter, and with blizzard conditions outside Sloth is quickly frozen. After freezing Sloth, Olivier orders Buccaneer to put the Elrics into the fort's holding cells so she can question them later. The next morning, the Elrics are thanked by several soldiers for helping during Sloth's invasion, but the soldiers still wouldn't let the Elrics out of their cell.

Hoenheim recalls when he left the Elric's house, lamenting that his body would outlast his family's. Meanwhile, soldiers investigating the tunnels under Briggs find themselves killed by a mysterious shadow. Lt General Raven tells Olivier to put Sloth into the tunnel and seal it off. Whilst Miles stalls Kimblee for time, Olivier kills Raven. As Olivier enters the tunnel via a separate entrance, Kimblee brings Winry over to see Ed and Al, reminding them of their place. Meanwhile, Scar reunites with Marcoh and Mei, and Roy gets information and a message from Olivier from his intel sources.

Winry fixes up Ed's automail before Kimblee talks with him, ordering his men to keep Al separated from him. Olivier sends a search party down the tunnels, who find a couple of survivors warning them not to put any lights on. Riza learns that Bradley's son, Selim, is a homunculus named Pride who attacks from the shadows. Kimblee orders Ed to search for Scar and Marcoh and create a bloody crest similar to Ishbal in Briggs, tempting him with a Philosopher's Stone if he accepts. After telling Al and Winry all about it, he grudgingly accepts the job, though doesn't intend to use the stone himself. As Ed and Al go to search for Scar, their real intent to find May as well, Winry decides to accompany them.

Riza gets a call from Roy, but is unable to say anything in fear of being watched by Pride. In the town of Baschool, Ed and Al, along with Winry, lose the guards that were assigned to them and end up running into May and Marcoh. Meanwhile, Scar encounters a couple of Kimblee's men, a pair of chimeras, and runs into trouble with them. Scar gets pinned, but Ed and Al arrive and beat the chimeras, before restraining Scar themselves. Winry and Miles arrive, and Winry confronts Scar face-to-face about her parents' deaths. Explosions then take place and it appears that Scar has taken Winry hostage. Meanwhile, as Olivier's squad retrieve the survivors from the tunnels, Briggs is approached by some people.

When faced with the option of judging her parents' killer, Winry decides to heal Scar's wounds, knowing it would be something her parents would do. Miles explains to Scar that he joined the military to gradually change the way people think of Ishbalans. Since Marcoh and May need Scar to decipher his brother's research, Miles offers to hide everyone at Fort Briggs, with Al insisting on sparing the two chimera. While Marcoh and company head for Briggs via tunnels in the mines, Winry comes up with rouse to make it look like Scar has kidnapped her to elude Kimblee just before a blizzard sets in. However, as Marcoh's group heads for the fort, Miles gets word that Olivier is no longer at Briggs and the fort is being manned by Central people. Al goes into the blizzard to find Marcoh's group and warn them. While in the blizzard, Al briefly sees his body, and wonders if it is trying to get its soul back. Meanwhile, Father makes plans involving Ed, Al, Hohenheim, Izumi, and one more candidate.