At midnight, there emerges a mysterious phenomenon known as the Dark Hour. This hidden hour, often overlooked by most individuals, poses great danger to those who are not entombed during this time. Those unfortunate enough to be conscious during this period encounter malevolent entities referred to as Shadows. However, a select few possess the ability to harness Persona - a unique power that enables them to combat these sinister beings. This elite group, known as SEES (Specialized Extracurricular Execution Squad), is tasked with investigating the cause of the Dark Hour's emergence.
Shortly after transfer student Makoto Yuuki arrives at Iwatodai Dormitory, his Persona awakens following an attack by a powerful Shadow. As a result, he joins SEES in their fight against Shadows and works to safeguard humanity from the enigmatic Dark Hour.