The theme of Innocent Sin, as with the previous entry, was exploration of the human psyche and the main characters discovering their true selves. The central character theme of Innocent Sin was the growth of teenagers and how they overcome their personal troubles. Another key element was the "power of Kotodama", the Japanese belief that words can influence the physical and spiritual world, with this power manifesting in the world of Persona 2 through the spreading of rumors.
The exploration of human psychology and characters discovering their true selves mirrored the previous entry's theme. The central focus of Innocent Sin was teenagers' growth and overcoming personal challenges. Additionally, a key element was the "power of Kotodama," where words had the ability to influence both physical and spiritual worlds, as seen in Persona 2 through rumors.