Tokiko and Gota stray from Kazuki after getting caught in an explosion created by Hiwatari. Meanwhile, the search-and-destroy team tracks down Victor and launches a full-scale attack, but Victor's Buso Renkin proves too powerful.
Kazuki is revived courtesy of the black kakugane's power. But to deal with the black kakugane, Kazuki must go to the place where Tokiko discovered it. Elsewhere, Tokiko informs Kazuki that she will not leave his side.
Shusui flashes back to his earliest memories. Here, he recalls being abducted by a woman claiming to be his mother and the days he spent in confinement, as the twins grew up never questioning the closed world in which they lived.
Kazuki and the Hayasaka twins are shocked upon learning each other's identities as Alchemist Warrior and LXE. Elsewhere, Kazuki proposes a showdown with Shusui, and Ouka is tasked with shutting down the school's security system.
Captain Bravo of the Alchemist Army recruits Kazuki to be a warrior. Meanwhile, Tokiko anticipates underground enemy activities within Ginsei City and transfers to Kazuki's class; Bravo becomes the manager of the school dormitory.
A homunculus embryo lodges itself on Tokiko. With only a week remaining before she becomes a full-fledged homunculus, Kazuki and Tokiko desperately search for the creator of homunculus in order to obtain the antidote.
Kazuki and Tokiko return to the haunted factory where everything began. There, they find the remains of victims and a homunculus incubator, discovering that the homunculi made there lodge themselves onto humans and consume them.