Assault on South Headquarters is the thirtieth episode of the 2003 anime, in which Archer arrests the mysterious boy as a suspected homunculus and a furious Izumi storms the military base to free him, drawing Greed's chimeras and a disguised Envy into the fray.
At the Southern Slums, the disgraced former officer Yoki, reduced to living there after Ed got him discharged, watches Ishvalan refugees arrive, and Scar's master is assured they will be safe among fellow outcasts. Yoki recognizes Scar, though, and makes a call. In Dublith, the boy escapes Ed through a wall, and before Ed can follow, a lizard-like man named Bido approaches, citing Ed's interest in the Philosopher's Stone.
At Sig's shop, Archer's questions about the Elrics and Izumi draw only meat-shop replies, while Winry and Mason watch. Armstrong and Sig flex their massive frames, alarming the onlookers, but the two simply shake hands in mutual respect. Bido explains that Tucker told him everything and offers to take the brothers somewhere, then slips away as Archer and Armstrong arrive; Archer recognizes him as a chimera escaped from Laboratory 5. Armstrong stays silent about Hughes' death when Al asks after him.
The brothers track the boy to a rooftop, quietly confirming that his arm and leg are truly Ed's. Archer, spotting an Ouroboros mark on the boy's foot, has Armstrong knock him down and bind him, then explains they are taking the homunculus to South City for questioning, dismissing Ed's account of the limbs as absurd. Sloth phones Yoki to confirm that catching Scar will win back his commission. Bido relays the boy's capture to the Devil's Nest, and Greed, eager to recruit him before the other homunculi can, sends Kimbley into the base while keeping Dolcetto back.
Izumi returns enraged, and when Al presses her about the boy, she coughs blood again and Sig rushes her to a hospital, where doctors find her missing several organs, hinting she once attempted human transmutation. She and Sig then vanish, having gone to storm Southern Command. As Izumi cuts through the soldiers to free the boy, Sig tells Winry how Izumi, years earlier, lost their stillborn son and then her organs and fertility trying to revive him. Kimbley blasts a hole in the wall for himself and Bido, and the confrontation becomes a four-way standoff once a figure appearing to be Fuhrer Bradley, actually Envy in disguise, arrives, while the real Bradley sends the Mustang Unit after Scar. In the slums, Scar notices an exiled Ishvalan whose tent bears a symbol matching his own tattoo.
The episode adapts the chapters Master and Apprentice, To Meet the Master, and A Fool's Courage. Greed first mentions the homunculus Pride here, though that identity stays hidden for another ten episodes.
The muscle-flexing scene between Armstrong and Sig comes from A Fool's Courage, but the anime swaps in the series-exclusive Frank Archer as Armstrong's companion rather than the Fuhrer, who in the manga wears vacation clothing instead of a uniform.

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In Assault on South Headquarters, Archer arrests the boy after spotting an Ouroboros mark on his foot, suspecting he is a homunculus, and has Armstrong bind him for questioning at South City despite Edward's objections.
Izumi Curtis storms Southern Command in a rage to free the captured boy, cutting through soldiers to reach him after learning of his arrest.
In Assault on South Headquarters, Sig tells Winry that Izumi lost a stillborn son years earlier and then lost her organs and fertility while attempting to revive him through human transmutation.
The homunculus Envy disguises himself as Fuhrer Bradley and arrives at Southern Command, creating a four-way standoff with Izumi, Kimbley, and the pursuing soldiers.
Assault on South Headquarters adapts three manga chapters: Master and Apprentice, To Meet the Master, and A Fool's Courage.
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