The second movie ended with Gluttony (Shinji Uchiyama), the Homunculus, swallowing Ed (Ryosuke Yamada), Envy (Kanata Hongo), and Ling Yao (Keisuke Watanabe). They end up in a mock Truth Portal with no exit. Ling Yao and Ed provoke Envy accidentally, and Envy changes form into a monster to target them.Al (Atom Mizuishi) and Gluttony sit outside, lost in contemplation of their next move.The movie begins discussing the identity of the secretive Van Hohenheim (Seiyo Uchino), Father of Al and Ed. Van Hohenheim tells a lady that anybody who returns from the Gate of Truth is a candidate for human sacrifice. He refers to the Promised Day, which will soon be upon mankind. Van Hohenheim says that if does not win, the country and all its people will be erased.A face-off begins between Ed, Ling Yao, and Envy. Ed and Ling get tossed around by Envy's monster form in retaliation; however, the fight stops, and Envy returns back to his original form when Ed finds a way out. Ed finds a human Transmutation circle inside the Truth Portal. Ed plans to perform a human Transmutation on himself, which he believes will open the portal and allow then to escape.Meanwhile, Al accompanies Gluttony to meet his Father to bring back Al, Ling, and Envy. Scar and May follow them, as Scar wants to know the truth.Gluttony goes to a network of tunnels under Central and reaches a chamber which houses the blonde (whom Gluttony calls The Father) controlling Bradley from the 2nd movie. The Father is an exact replica of Van Hohenheim.On the other hand, Mustang (Dean Fujioka) prepares for a coup and tries to figure out if any of the generals are against the Homunculi and knows that Bradley (Hiroshi Tachi) is a Homunculus. Mustang realizes that entire military is corrupt. Bradely tells Mustang that he is a human turned into a Homunculus, called Wrath.Ed, Ling, and Envy eventually escape from Gluttony's portal. The Father uses blood from the Philosopher's Stone to convert Ling into a Homunculus. Ling ends up sharing his body with Greed. With the help of the Greed, they reunite with Scar (Mackenyu) and May (Risa Mei) and escape The Father. They set out to find out about the plans of the military and the Promised Day.Ling tells Ed that on the Promised Day, The Father plans to open The Door.Scar and Mei wrap their minds around what Scar's brother had left behind, and they find out it was a flipped Transmutation circle. Each point on the circle mapped to a city on the map of the country. Each city was where riots recently took place, including Ishvalan. If the circle is as big as the entire country, countless lives would be sacrificed. They reckon Hughes knew this and was killed as a result.The flipped Transmutation circle would nullify the Transmutation circle and save all lives. Scar's brother had figured this out by studying both Xing and Amestris alchemist knowledge.With the preparations in place, they find out that the military has been preparing for the Promised Day and that Bradley was helping out his Father. Only the city of Briggs has not yet been taken by Bradley and is thus his next target.Ed sets out to enlist the help of General Armstrong (Chiaki Kuriyama), who leads the Briggs army. Armstrong agrees with Ed when a Homunculus attacks her base. Armstrong then discovers a huge tunnel underneath the length of the country that runs directly under her army base.This is when General Raven arrives from Central and starts a war with Drachma, the mortal enemies of the Briggs. Armstrong has no option but to retaliate. The Transmutation Circle is now complete.Armstrong goes to Bradley and pretends to pledge her allegiance to him to gain access to his inner circle.Al finds Van Hohenheim who tells him about The Father.The "Dwarf in the Flask" is the Father of the Seven Sins. He created these Seven Homunculi after he experienced emotions, although he had none, and not being able to feel any served as his downfall. He experienced these emotions through Van Hohenheim, Ed, and Al's Father, who he had saved from slavery and offered to help him if he was helped.Van Hohenheim and Father are intricately related, which also makes the Homunculi Van's children as well. Father or The Dwarf in the Flask had escaped and used Van to get to the King of Xerxes obsessed with Immortality. During the spell, the Father turned on the King and takes over the souls of half the people in the Kingdom.Father was already joined to Van, thus not killing him off. He took over the King and created a new body for himself modeled on Van and took over the lives of his citizens to fuel his plans to get the power of God.Van realized his mistake and set out to correct his wrongdoings by formulating a plan to overthrow and nullify his Father's plan. Van presents himself to the Father, who proceeds to takeover the power of 536,239 souls inside the Resurrection Stone that Van has. Van could not stop Father from attaining the power of God but instead made the souls that were already inside him, due to the takeover, comply with his plan and destroy Father from the inside. But this only destroyed Father's body, and he reverted to his Dwarf in the Vessel form, only grown up now.Al and Van together link up with Ed. They are attacked by Selim (who is a Homunculus named Pride). Van entombs Al and Selim both inside a prison made of Earth, where Pride cannot use his powers.Meanwhile Armstrong and her army start the attack on Central. She is helped by her older brother Alex Armstrong to help fight the Homunculus.Selim (Kokoro Terada) (Bradley's adopted son), who is actually Pride, is rescued from his tomb by Gluttony. But Selim kills Gluttony to take his power.Ed and Scar follows the tunnel and finds an army of Homunculus hiding behind a door. This is when Mustang arrives to burn the Homunculus. Envy changes into his monster form and attacks Mustang. Mustang easily defeats Envy and takes away his eyes. But Ed intervenes and prevents Mustang from killing Envy. Envy kills himself off because he feels insulted that the humans were pitying and letting him go considering the difference in their strengths.In order to begin the Human Transmutation so that Father can gain power, Selim arrives to start a ritual of human sacrifice that will bring upon the Promised Day. Mustang is forced to take part in the ritual, which results in Truth taking away his eyes.The ritual had 5 sacrifices: Van, Ed, Izumi (Ed and Al's alchemist teacher, Mustang, and Al). As the Transmutation circle is completed, the portal opens which unleashes the Dwarf in a cosmic proportion and who absorbs the power of the sun.Van now uses the shadow of the moon on the Earth to launch his own Transmutation circle. This returns the souls absorbed into Father back to the people of Central.Then Scar activates the flip Transmutation circle to remove Father's excess powers.Mustang then rejoins the group without his eyes, and Riza (Misako Renbutsu), his trusted subordinate, helps him fight by being his eyes.Greed got sucked into Father for his powers. However, he assisted Ling Yao in defeating Bradley, who is also Wrath. Bradley is eventually killed by Scar. Selim is killed by Ed.One by one, all of the Homunculi lost their lives, and Father himself was forced to retreat back into his prison. However, Mustang does not regain his eyesight back and Riza offers to become his eyes until they find a way to get his eyesight back from Truth.Van can sense that Father is reaching close to the limit of his powers.At almost the end of the battle between Father and Ed, Father has weakened considerably. However, Ed gets stuck to the wall with no way of fighting or escaping. Alphonse has no way of saving Ed due to Ed's metal hand being destroyed in the after-effect of Father's counter-attack.Al, with the help of May's alchemy, sacrifices his soul and returns back to the empty shell of his body, waiting with Truth to save Ed. Ed regains his arm back, just in time to save himself and also to end the battle once and for all.Van offers to sacrifice himself to bring back Al, but Ed refuses and instead sacrifices his beloved Alchemy to bring back Al intact. Truth accepts the sacrifice, calling it worthy, and lets Ed take Al back to their realm. Ed is overjoyed to have his brother back, and the group celebrates their victory. The citizens gain back their lives, and the city returns to its glory. A budding romance begins between Winry and Ed.Van helps Ed and his group defeat the monster, Father, who had attained the power of God, and ultimately sends him back through the door in the portal of Truth where he belonged, putting an end to the decades of suffering that he had brought along.The movie ends with Al returning to Ed and his friends after Ed's sacrifice and Van Hohenheim dying peacefully in front of his wife's grave.