As Kazuki begins to learn more about his enemy and the source of his power he decides to assist Tokito in the eradication of the Homonculi in his town. As Tokito begins investigating the “haunted factory” of the Homonculi she discovers a very disturbing thing, apparently the Homonculi have been developing a new weapon, a parasite that turns people into man eating monsters.

Muto Kazuki and Tsumura Tokiko are investigating who is behind all the homunculi appearances and hostile acts. Only with two leads: He wears a Papillion Mask and attends Kazuki’s high school. With that in mind, Kazuki and Tokiko do a thorough search of the high school–searching for more leads as to who this mysterious ” Papillion Mask Creator ” is.

After searching hard for the Papillion Mask, they finally found him–although he was definitely not what they were expecting. He supposedly wanted to bargain with Kazuki: the antidote to the Homunculus attached to Tokiko’s body for his Busou Renkin, but Kazuki refused. With a single Kazuki punch, The Papillon Mask was knocked out and brought to be questioned. (The “antidote” was a fake.

Kazuki and Tokiko retreat to form a plan on how to defeat the eagle Homunculus but not all goes as planned when Tokiko receives possibly critical injuries. Hurt but not out for the count the eagle Homunculus plans to target Tokiko, but Kazuki won't hear of it and they face off in an exciting and explosive duel. Kazuki learns the reason behind this Homunculus's awesome strength is quite similar to the source of his own will to fight. When the battle turns against him and all seems lost Kazuki decides to go for broke and unleash a powerful but dangerous attack.

Kazuki finds Koushaku in his great-great grandfather's laboratory and attempts to destroy the Homunculus matter. However, due to the interference of Koushaku's younger brother, Koushaku is able to have the Homunculus matter attach to him and is turned into a Homunculus. He then begins to eat everyone in the vicinity until he is killed by Kazuki, who passes out from exhaustion before he is able to deliver the cure to Tokiko. Kazuki awakens to find that Tokiko has been cured and that his buso renkin shall be called Sunlight Heart.

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.