Captain Bravo, a member of the Alchemist Warriors and the one who delivered the cure to Tokiko, offers Kazuki to join their mission on combating against the LXE, a group consisting of Human-type Homunculi based in Kazuki's town. Koushaku, having been resurrected by the LXE's leader who is also his great-great grandfather, Dr. Butterfly, and now calling himself Papillon, seeks Kazuki and declares war on him. Kazuki, Tokiko and Bravo are then attacked by Kinjo, a Homunculus of the LXE, but he is quickly dispatched by Bravo.

During the night, Bravo takes Kazuki out to the woods for special training while Tokiko protects the kakugane acquired from the previous battle. Later on, a Homunculus named Jinnai uses a buso renkin and takes control over the students in the dorm, ordering them to take the kakugane from Tokiko. Tokiko is able to avoid her classmates and kill Jinnai, freeing them from his control. Papillon takes the kakugane from the defeated Homunculus, declares that he will defeat Kazuki and then leaves the scene.

Kazuki and Tokiko befriend the Hayasaka twins, Shusui and Ouka. However, the twins are actually humans working with the LXE ordered to kill the Alchemist warriors at the school. When two LXE Homunculi invade the school, Kazuki and Tokiko intercept the threats, causing the twins to realize who the Alchemist Warriors are and that they must kill their friends.

The four begin to battle and Kazuki eventually inflicts a fatal wound on Shusui. Ouka uses her buso renkin and heals Shusui while at the same time receiving Shusui's wound on her own body. Due to this, Kazuki realizes they are both humans and not Homunculi and questions whether they are the enemy or not. Shusui reveals that they worked under the LXE so that one day the two can become Homunculi and live together for eternity.

Tokiko proceeds to eliminate the twins but is stopped by Kazuki who argues that they are still human and deserve to live. Shusui inflicts a critical wound on Kazuki while he is distracted. However, Ouka uses her buso renkin and absorbs Kazuki's wound damage claiming that Kazuki is someone they can trust. As Ouka begins to die, Kazuki, Tokiko, and Shusui are able to avert her death with the healing properties of the kakuganes. The next day, Kazuki and Tokiko visit Ouka in the hospital who reveals that her brother had left to train in order to rid himself of LXE's corruption.