En-Fem-E No. 9 sees the main character start out as a normal college student. His adoptive parent’s relationship is on the rocks and the main character and his father move in with his fathers new mysterious girlfriend. When the father is suddenly called away on important unknown business the manipulative transformation at the hands of his father’s new girlfriend begins. Part one wraps up with the main character accompanying his new mistress to Tokyo where he/she falls into the grasp of a nefarious pharmaceutical company with dubious and sinister plans for the main character’s future.