Prior to the present, Lily was born as the daughter of the village lord and a prostitute from Sabasa. She and her mother were bullied by the other villagers due to being outsiders, to the point that when her mother died, they refused to give her a proper burial. Lily's life did not improve when she was moved to her father's mansion, as her family also mistreated her. To take revenge, she studied magic from forbidden books and, five years before the present, she used this power to kill her father and brothers. Now the lord of the village, she started the witch hunts to capture villagers as subjects for experiments.
At some point (it is unclear if this was before or after Lily took over as lord), a female villager named Lucia went to the national university in Sabasa to study Magical Science. She later returned to the village and was made another one of Lily's subjects.
After several years of experiments, Lily was able to implant tentacles in her own arms.
In the present, Luka and Alice arrive at the village. A female villager tries to warn them not to enter the village, but is interrupted by the arrival of two guards. The guards accuse Alice of being a witch and subject her to a test: drawing a knife across her hand that, supposedly, will not cut her if she is a witch (though the knife is actually a trick knife that cannot cut people). Alice uses her unique biology to create a cut on her hand, frightening the guards as they think that she's actually a witch. They speak to the villagers to gather more information, then Luka heads to the mansion alone. He uses Sylph's power to blow off the guards' helmets, frightening them as they think he's a witch as well.
Luka enters the mansion and encounters Lily herself. She explains the truth behind the witch hunts and her intention to make him another subject, then escapes through a nearby door. Luka chases after her. He encounters Lily's victims: female villagers transformed into tentacle monsters (including Suck Vore, Worm Villager and Iron Maiden, and the male villagers being used as semen sources. He is forced to fight the former. Eventually, he catches up to Lily and succeeds in defeating her.
The captured villagers are freed and Lily herself is placed in prison. However, many of the villagers are dead, with Lucia believed to be among them. Furthermore, the female villagers still have their tentacle arms, though they are able to hide them from the others. Luka and Alice leave.
Unknown to everyone else, Lucia actually survived. She escapes the village, now with a distrust of humans, and eventually meets up with the angel scientist Promestein. She studies under Promestein and manages to create her own version of Homunculi.
Later, Goddess Ilias (Promestein's superior) declares war on humanity. As part of this, Lucia takes her custom-made monsters and attacks Witch Hunt Village. She visits Lily in her cell, taunts her and then devours her.
Luka and Alice return to the village. The female villagers reveal their tentacles and fight against Lucia's forces. After defeating Chimera Homunculus and Iron Maiden v2, Luka confronts Lucia herself. He defeats her and tries to convince her to change her ways. Lucia is reluctant to trust humans again, telling Luka to fight for her share and then leaving.
When Ilias launches a second attack, this time Lucia comes to assist the village's defense.
After Ilias' defeat, Lucia works in the mansion disposing of the dangerous chemicals and equipment. Luka and Alice visit and they have a discussion with Lucia about Promestein and the ethics of human experimentation.