Dr. Shaft belongs to the thirteen Apostles, scientists who forcibly fuse humans with animals in unethical experiments to create superior "Newmen." He shares their conviction of divine selection to engineer humanity's successors. His experiments targeted his own family: his wife Shizue fused with bear, lion, snake, and eagle, while his son Shinichi underwent similar procedures but was deemed a failure due to youth and expendability. Shizue died resisting to protect Shinichi, causing the laboratory's destruction.

Dr. Shaft escaped with the Apostles aboard a flying ark, avoiding accountability. Operating under biblical aliases like Abraham and Judas, the group views itself as architects of a new world. Their experiments produce grotesque "Demonic Beasts" exhibiting extreme body horror, such as growing siblings from one body or sentient gas within bandages.

His past connects to the Tengai family; the Apostles destroyed their village, killing Tomisaburo and Maria Tengai's parents. Maria, valued for her psychic abilities, is targeted for her perceived role in ushering the Apostles' new era. Dr. Shaft's actions catalyze broader conflict, driving Shinichi to hunt him and the Apostles for vengeance. His motivations remain rooted in scientific fanaticism and unwavering allegiance to the Apostles' collective goal.