In this special, they look back at what has happened so far.
It has been two years since Edward Elric was taken from his home to the Gate of Alchemy in 1923. Edward researches rocketry in Munich, Germany along with his friend Alfons Heiderich, a young man who resembles Edward's brother, Alphonse. Edward saves Noah, a gypsy from being sold. She's taken in and lives with Edward and Alfons. Edward helps to hunt down a dragon for inspiration for a film. However, Edward is captured by the Thule Society, which is led by Karl Haushofer and Dietlinde Eckhart.
They capture Edward's father, Hohenheim and open a portal to the world Edward knows. They emerge into a city called Liore. Alfons comes and fights off the armored soldiers. Edward breaks into the Thule Society headquarters and re-opens the portal to Earth. However, they are attacked by Gluttony. When the gate opens, Eckhart leads a brigade and a battle ensues.
Ed and Al learn about the real reason Ishbal was destroyed from an unlikely source; Ed also learns another secret that had been hidden from him, with mixed results.
Scar tells Ed the secret of his arm, how he knows Lust. Marta faces the Fuhrer and learns a terrible secret.
Ed tries to alert Mustang to Scar's plans for Lior while he learns about what happened since his last visit there.
Ed must deal with his past mistakes in the underground tunnel while the race is on to both complete the Philosopher's Stone and save Al.
Ed and Al are on the run, having been declared fugitives and wanted criminals by the Fuhrer, who sends Col. Mustang and his team to capture them against their own beliefs. Meanwhile, Winry is surprised to see a man who mistook her for her mother show up at Pinako's door.
As the homunculi gather under the presence of their leader in Central, The Elrics reveal a long-hidden truth to Mustang and the others in Resembool. At Pinako's, a man from Ed and Al's past gives both the boys and Mustang sound advice on the creation of homunculi, and Ed and Al finally learn the truth about Hughes.
As Mustang tests the information he discovered in Resembool in front of the military council, people from the Elrics' past come into play: Al gets a mysterious phone call from one while Ed goes to visit another, hoping to find a way to defeat the homunculi and their leader.
As Ed tries to discover the truth about the leader of the homunculi, he runs into Wrath and Lust with interesting consequences. Meanwhile, the obsessed Tucker puts his plans for Al in motion as Mustang and Armstrong are sent up North for yet another battle
Ed locates Al just as Sloth decides to be rid of the Elrics once and for all. A showdown between the Elrics and three of the homunculi finally prove the truth about memories...and homunculi.
As Al is taken prisoner by one of the remaining homunculi, Ed and Izumi go off in search of answers that might lead them to where the master of the homunculi might be keeping him. Meanwhile, Mustang's plan is put into action, old friends and enemies return, and Ed and Mustang have a chance meeting in which both come to terms with their decisions.
Ed travels to the lost city underneath Central and comes face-to-face with the master of the homunculi. Meanwhile, loyalties are drawn within the military and a captive Al ponders why he has escaped death for so long.
On the other side of the Gate, Ed finds himself in a world that, while much like his own, has some major differences. There he finds his father, who finally reveals the truth about his past actions---and of alchemy in general.
There is much going on in Ed's absence, however; in the underground city, Dante puts her plans for Al into play and turns Gluttony into a horrific creature while Mustang puts his own plans for the Fuhrer into action.
In the series finale, both Ed and Al finally learn just how much they are willing to give up in the name of both Equivelant Exchange and each other. Also, Mustang's plans are aided by an unlikely source as Dante's are thwarted by one of her allies.