Ed and Al have decided to head out on a trip without telling anyone. The two brothers leave Central City, deciding to seek out the possibility of meeting their master. On the other hand, Hughes continues his investigation concerning the 5th laboratory and the Philosopher's Stone. Doing so, he arrives at a conclusion, but this time...
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Hughes visits Mustang in his apartment and finds it in complete disarray. He finds that Mustang is studying material considered taboo. After the war, Mustang falls into a depression. However, this is Hughes dreaming of the past, for he is woken up by the Fuhrer.
Back at the Fuhrer's office, he reveals to Hughes that he suspects Gran teamed up with some Ishbal remanants to conduct dangerous research.
Unsatisfied with the Fuhrer's findings, Hughes receives permission to further investigate the incidents at the 5th Laboratory. He implies that there is still a faction within the military that wishes to create the Philosopher's Stone.
Wanting to ask Marco a few questions, Hughes is informed by Juliet, the Fuhrer's secretary, that he is in Central City. Only she knows where he is.
Hughes takes the information he gathered to Ed and Al. However, they have decided to look for an alternative to reach their goal. They plan to head to Dabris, where their former teacher lives. Winry pleads and finally is allowed by Ed and Al to accompany them. She is excited because the mecca of auto mails, Rush Valley, is on the way.
On the train, Winry finds out that the brothers are not headed to Dabris, for the memories of their teacher seem scary. They will, however, visit Rush Valley. Instead, Ed wants to go to a large Ishbal camp in the south.
In the middle of the desert, the Ishbal survivors stop for the night to rest. It is there that Scar's master pays Scar a visit. He tells scar that revenge only leads to more revenge and that he is merely taking out his anger on strangers. In the middle of their reunion, they are attacked by a bunch of hoodlums.
Scar steps outside for a moment and dismounts one of the riders from his bike and kills him instantly. Killing another one in quick succession, Scar forces the rest of the gang to retreat.
Meanwhile, Mustang finds out that the Elric brothers were hospitalized for a short time. Realizing that something is going down, Mustang books a train to Central City.
At home, Hughes says goodnight to his wife and daughter and leaves to investigate something.
Back at the office, Hughes makes an important connection. A squadron by the name of Douglas started the civil war in Ishbal. Coincidentally, the Fuhrer's secretary has that last name. He heads to the hotel to meet Marco as informed by Juliet.
At the hotel, Hughes has made serveral important connections regarding the identity of Juliet Douglas. About to open the door to Marco's room, Hughes is stopped by Lust who intends to kill her. Saved by Ross, the two run away.
Hughes, on the brink of a potential information coup, calls Mustang with information that could send Mustang to the top. Turning around, Hughes confronts Ross. Discovered, Hughes strikes a suppseoly fatal blow only to discover Ross transform into his wife and shoot him.
Falling to the ground, Hughes remembers back in Mustang's promise to become the Fuhrer and change the way the country is run. Back then, Hughes promised Mustang to work as Mustang's subordinate and push Mustang upwards.
At the funeral, Mustang was promoted two ranks to Brigadier General Hughes. In the end, Glacier, Elysia, Mustang and the others watch as Hughes is laid to rest. Hughes perhaps withheld information from Mustang so that Mustang could head to the top without any worries.
On the train to Rush Valley, Ed catches a glance of Hughes waving to him on the train platform.