Kazuki Muto, a high school student, sacrifices his life to save Tokiko Tsumura, a warrior wielding a lance-like weapon called a Busou Renkin, from a homunculus attack. Tokiko revives Kazuki using a Kakugane, a core that generates Busou Renkin, which transforms into a weapon tailored to the user's fighting style. Kazuki's Kakugane manifests as a sun-shaped lance, the Sunlight Heart. The two form an alliance to combat homunculi, monstrous beings created by alchemy that feed on humans.

The narrative unfolds as Kazuki and Tokiko join forces with the Alchemist Army, an organization dedicated to eradicating homunculi. They face the Homunculus Master, a powerful entity leading the homunculi, and his subordinates, including the enigmatic Papillon Mask. Kazuki's determination to protect humanity and his growing bond with Tokiko drive the story forward. Along the way, they encounter allies such as Captain Bravo, a skilled alchemist, and Gota Nakamura, Kazuki's loyal friend who becomes involved in the conflict.

The plot delves into themes of sacrifice, redemption, and the consequences of alchemical experimentation. Kazuki's journey is marked by his struggle to balance his newfound responsibilities with his desire to live a normal life. Tokiko, initially driven by duty, gradually opens up emotionally, revealing her tragic past and her connection to the Homunculus Master. The series explores the moral complexities of alchemy, as characters grapple with the ethical implications of creating life and wielding immense power.

As the conflict escalates, Kazuki and Tokiko confront increasingly powerful homunculi, culminating in a final battle against the Homunculus Master. The resolution ties together the characters' arcs, emphasizing the importance of human connection and the resilience of the human spirit. The series concludes with Kazuki and Tokiko continuing their fight against homunculi, their bond stronger than ever.