Having learned that the Philosopher's Stone is made of live humans - and worse, that it would take several human lives in order to fashion a single Stone - the distraught Edward and Alphonse ask Sgt. Brosh and 2nd Lt. Ross to disavow knowledge of their discovery.
Meanwhile in East City, after Scar's jacket is found by military police near the wreckage of the sewer tunnel where he had encountered Gluttony, Colonel Mustang and his men are summoned to the scene to investigate. Though Lt. Hawkeye determines that the bloodstains on the jacket suggest that the serial killer must have been badly injured, Gluttony laments from nearby that his prey managed to escape him. Lust consoles him while making plans to return to Central City and inform their Father of this new development.
Back in the capital, Ed and Al mope in their hotel room, cursing their luck and wondering if their original forms are forever lost to them. Edward mentions to Alphonse that there is something important he always wanted to discuss with his little brother but was too afraid to bring up. However, Edward is interrupted when Major Armstrong bursts into the room, having pressured Brosh and Ross into telling him why the boys have been so glum. As Armstrong weeps over the boys' misfortune and laments how cruel the truth can be, Edward is suddenly reminded of Dr. Marcoh's cryptic final message - that there is a "truth behind the truth". Taking this to mean that there is something else yet to be discovered, Edward resumes his investigation with the help of the others. Looking at a city map which denotes all of the four Alchemical Laboratories currently being operated in Central City, Edward notes a supposedly abandoned Fifth Laboratory within the city limits and proposes that this site is most likely the facility at which Philosopher's Stones were being manufactured - citing its adjacence to Central Prison as a key, since death row inmates could conceivably have been used as the Stone's necessary "live ingredients" without attracting attention. Wondering if the laboratory's alleged actions are connected to the military or merely an isolated incident, Alphonse asks the Major who was in charge of Lab 5 before it was shut down and Armstrong informs them that the facility was previously under the jurisdiction of State Alchemist and Brigadier General Basque Grand, but that Grand - along with several other alchemists who may have known the truth - had recently been assassinated by Scar. Major Armstrong mentions that the situation could become particularly complicated if a Brigadier General or someone of even higher rank were involved and prepares to investigate the matter quietly on his own, advising Brosh and Ross not to speak of this to anyone and demanding that the Elric brothers remain in their hotel and keep away from Lab 5 until further notice.
Under cover of night, however, the boys sneak away to investigate the facility - curiously discovering that a soldier has been placed outside as a guard despite the building being supposedly "abandoned". Realizing that the only covert way into the lab is through the narrow vent system, Edward opts to head inside while Alphonse remains without. Deep within the recesses of the empty lab, two armor-clad, shadowy figures calling each other 48 and 66 sense the intruders and stir; 66 makes plans to go after Al while 48 prepares to take Edward on. Noticing that the facility still has electricity being fed to its lighted hallways, Ed confirms that the lab is still in use. Meanwhile, 66 descends upon Alphonse - attacking him with a meat cleaver and remarking that, while 66 is his given codename, his true identity is a shocking secret.
Edward reaches a large hall inside the lab and notices a huge, bloodstained Five-Point Transmutation Circle on the floor. He asks himself aloud if this is where the Philosopher's Stone was created 48 answers in the affirmative, emerging from the shadows to inform the intruder that his presence here cannot go unpunished, especially since he appears to know about the Philosopher's Stone. Transmuting the outer plating of his automail arm into a blade, Edward engages 48 in battle and discovers that the armor-clad swordsman is, in fact, an empty suit of armor just like Alphonse. 48 explains that he was a serial killer known as "Slicer" who had been placed on death row upon his arrest and used as a test subject in Soul Binding experiments. He shows Edward that his own Blood Rune is hidden inside his helmet and informs young Fullmetal that he must destroy the rune to win before preparing for a second assault.
- In this chapter Edward mentions having visited Laboratory 3 shortly after receiving his certification, but not noticing anything strange. Additionally, it is noted that Lab 3 was the facility with which Tim Marcoh had been affiliated.
- In this chapter, it is first explained that Blood Runes function by binding the iron in the blood to the iron of the armor body.