Munich, Germany, 1923. Two years have passed since Edward Elric was dragged from his own world to ours, leaving behind his country, his friends and his younger brother, Alphonse Elric. Stripped of his alchemical powers, all this time he has been researching rocketry together with Alphonse Heiderich, a young man very much resembling his own brother, hoping to one day find a way back home.

His efforts so far have proven fruitless, but when he hears that the Thule Society, an occult group strongly tied to the Nazi Party, discovered what could be a clue to the location of the legendary, mystical place called Shamballa, Edward's hopes are renewed. Meanwhile, in his own world, Alphonse Elric ventures deeper into the mysteries of alchemy in search for a way to reunite with his older brother.

Ed and Al demonstrate what they will sacrifice for each other.

Ed battles Envy in order to free Al.

Ed is sent to the other side of the gate, where his understanding of alchemy is questioned.

When Al gets kidnapped, Ed must rescue him; Mustang helps Ed.

Tucker tries to resurrect his daughter; Sloth captures Al.

The brothers find themselves in danger while separated.

The truth behind the truth is revealed; Colonel Mustang decides to challenge military leadership.

Ed and Al must convince Mustang's faction that the Fuhrer is not what he seems.

Ed and Al begin their journey home; the Fuhrer declares the Elrics to be fugitives.

Scar remains determined to create the Philosopher's Stone.

Al intervenes when Marta tries to get revenge on Kimbley for her friends' deaths; the seventh sin is revealed.

Marta leads Ed and Al to the ruins of Ishbal, and she tells them the true cause of the war and the reasons for her transformation; Ed and Al question everything they once believed.

Al questions Ed on their mission, creating tension between the two brothers; Sciezka and Winry come into contact with the dangerous Sloth.

Mustang gets investigated; an adventure with the Flame Alchemist and his loyal followers; mystery unfolds unknown relatives of Maj. Armstrong, and a haunted warehouse.

Lust and Gluttony meet with Wrath for the first time; Ed, Al and Winry travel to Ishbal and continue to crack the mystery.

Lust wants to know where she came from, and where she will go when she dies; Lust meets a familiar man who provides answers and memories.

Greed transforms his body into an impervious shield and tells Ed he must kill him in order to save Al; Armstrong battles Greed and his men.

Kidnappers take Al, leaving Ed frantic.

Izumi sends Ed and Al to meet the alchemist Dante.

Izumi escapes with the boy; the brothers try to stop Izumi's plan of atonement.

A former military officer spots Scar; Izumi attacks the military.

The brothers encounter a strange boy.

Hohenheim's visit ends with a harsh warning to Pinako; Ed finds hope and has confidence that Al can be returned to his body.

Ed and Al are reunited with Izumi, their former teacher who gives the boys a traumatic interrogation.

Winry drags Ed and Al to Rush Valley.

Ed and Al give up their search for the Philosopher's Stone.

Al joins Scar on a renegade mission against the state.

Winry needs to make repairs; Al questions his existence.

Ed is nearly tricked by a face from his past.

Ed discovers more about the experiments in the fifth laboratory.

Two guardians of Lab 5 unleash an assault on Ed and Al.

Ed and Al learn the secret ingredient for the Philosopher's Stone.

Ed and Al scour the library for Dr. Marcoh's records; Scar battles Lust and Gluttony.

The Elrics return to their childhood village; Ed visits his monther's grave.

Ed and Al return to their hometown for repairs.

While on the run, Doctor Marcoh confess to the Elrics.

Ed and Al search for a deserter alchemist.

Ed challenges Mustang to a fight.

Ed and Al discover the source of the strange malady.

Imposters parade as Ed and Al.

Ed and Al stumble into an unpopular manhunt for a crowd-pleasing thief.

Ed is assigned to inspect the progress in a small mining town.

Ed resigns as State Alchemist; Winry arrives.

Shou Tucker must impress the state with his alchemy for his annual assessment.

Ed and Al prepare for their Alchemy exam.

Ed and Al are held hostage on a train.

While on their way to seek out a man from their early childhood, Al and Ed arrive in a town haunted by a ghostly woman.

The story line flashes back to a younger Ed and Al and tells how their mother died and their determination to bring her back to life.

Edward and Alphonse have to decide if they should reveal the truth behind Cornello's miracles and the possible devastating effects that revelation might have on the townspeople and their lives.

Edward and Alphonse meet a so-called religious leader during their travels who can invoke miracles, once seeing his miracles in person, they set out to discover if he is using the fabled Philosopher's Stone.