Ed goes home to Resembool to find Hohenheim, his father, standing at his mother's grave. After a brief argument, Hohenheim and Ed walk to Pinako's with Ed hostile and belligerent towards his father. While Ed pretends to be asleep, he overhears his father questioning Pinako on whether the body Ed and Al created by transmutation was Trisha revived. This question spurs Ed's curiosity, and after Hohenheim leaves the next day, Ed asks Pinako to go with him to the graveyard to dig up the body he and Al created so many years ago. He starts throwing up and has to take several breaks while digging, but eventually pulls up a lock of hair; black hair instead of brown. Pinako also points out that the bones aren't the same length as Trisha's were. So Ed learns that they didn't even bring back their mother, but brought back something entirely different.

Ed goes to central to find Al is missing his lower "jaw" and his right arm of his suit of armor. After Ed repairs Al, he finds out Al had a run in with Barry the Chopper and the homunculi, but also finds out that Al learned that the soul, when not placed in its original body, can reject the substitute body, just as the human body can reject organ transplants. This rejection may occur within seconds of the soul being placed on a new body, or may not occur for hundreds of years, but rejection is inevitable.

He tells Al and Winry, after asking about an incident when they were five, that he is confirming the memories Ed has that Al doesn't have. Al and Winry allude to a moment when Ed was unconscious and fighting a fever after surgery when Winry walked in on Al, who was "resting," and they talk. Only, when Al and Winry allude to the conversation, it sounds almost like they played multiple pranks on Ed, causing Ed to become irritated and ask them to stop talking.

When they get back to the conversation at hand, Ed theorizes that Al's body is with Truth inside the gate and that it's still alive and possibly connected through Ed and Al's blood to Ed. (That he is sleeping, eating, etc. for the both of them.) Al's brain is still alive inside a body that's still alive and it is collecting the memories since Ed transferred Al's soul to the suit of armor. At this point, Al also remembers when he opened the Gate of Truth, he found himself in there, rather than his mother, as he expected. He also realized that his soul was placed on the body that he and Ed had transmuted, and even saw Ed from the body's eyes. However, rejection took place almost immediately after his soul was placed onto the body. As a sidenote, because Al's body is biologically connected to Ed, Ed has enthusiastically hypothosized that he may grow taller once Al's body is recovered since he won't have to eat (or grow) for both bodies.

Ed and Al eventually figure the only way they're going to catch a Homunculus (and the philosopher's stone within them) is to let Scar attack them, and tries to attract Scar's attention. Ed does a series of do-gooding around town (while showing off as much and as loudly as possible to get Scar to notice him) and eventually succeeds. A fight between Scar, Ed and Al ensues, with Mustang and Hawkeye diverting attention from them by redirecting the military vehicles to different places away from where the real fight is happening. Winry goes looking for them and ends up overhearing Ed accusing Scar of killing Winry's parents. She picks up the gun an officer dropped and points it at Scar, only to have Ed jump in front of her and tell her to drop the gun while Scar descends on him from the front. When Scar sees this, he hesitates, remembering his own brother protecting him from Kimblee's attack during the Eastern War. Seeing his hesitation, Al attacks Scar, driving him away from the two.

Then, Ling ties up Gluttony and Winry is going to Rush Valley once more. Gluttony escapes his bonds and tries to suck up Roy and everyone else into his "gate" for a stomach. He ends up sucking up Envy, Ling and Ed, instead, and Al's left hand. Ling and Ed find Envy eventually and Envy actually tries to be nice to Ed, however, it all backfires and Envy turns into his true form.

The tortured souls in Envy's natural form cause Ed to have a semi-nervous breakdown (he cannot bear to hurt them and flashes back to Nina for an instant). Envy then swallows him. However, after seeing pieces of the Xerxes ruins in Gluttony's stomach and the philosopher's stone that is Envy's center, he kicks out one of Envy's teeth and tells Envy and Ling that he knows a way that they can escape from Gluttony's stomach.

In the recent chapters, Ed realized that while human revival is impossible, since equivalent exchange requires the existence of the soul in question, it is possible to open the Gate of Truth by transmuting existing humans using themselves as the starting materials. This does not violate the rule of equivalent exchange, but still is a form of human transmutation, and so is a way of opening the Gate of Truth. Using the souls inside Envy as the "Toll," Ed successfully transmuted himself, Envy, and Ling, and opened the Gate once more. This time, he sees a second Gate, as well as an emaciated Alphonse sitting in front of the second gate. Ed yells for Al's body to come with him. However, Al's body told Ed that he could not go with Ed back to the real world because Ed had a different soul (as in Al's soul must be there for the body to return from the gate). Ed is then swallowed by the hands reaching out from the Gate of Truth, and he, Envy, and Ling fall out of Gluttony's stomach, and in front of the Homunculi's "Father," who bears a startling resemblance to their own.

Unable to fight "Father", because somehow their alchemy was sealed, Ed and Al helped Scar and Mei Lei to escape but stayed behind, knowing they wouldn't be harmed by him or the Homunculi because they are still useful to them. They were sent to meet King Bradley, who told them to stay out of their affairs, if they wanted to guarantee Winry's safety, but also agreed to let them continue their search for a way to restore their bodies.

Intrigued by the fact that his alchemy was nullified by "Father", but Scar and Mei Chang's were not, Ed concludes that it must be because their alchemy has a different origin than his. He decides to look for a way to obtain knowledge about foreign alchemy.

In later chapters the Führer threatened Edward with Winry's life to put a stop to what he was doing. Edward went to see Riza, and told her about the threat, she said "You really love her don't you?" causing Edward to turn red and yell (and stutter) that he didn't. She laughs probably not believing him. So far she seems the only one who actually says (bluntly) that Edward may love Winry.