Persona 3 Em is an RPG for mobile phones designed as a side-story taking place during the Yakushima trip of Persona 3. It is designed to emulate the original game in having a social-interaction driven daytime period and a dungeon-crawling night period.

During the nighttime when the members of S.E.E.S. go to sleep they awaken in the "Nightmare Hour" which is similar to the Dark Hour from the main games. During this time they must explore a Tartarus-like dungeon called Oneiros, the entrance of which being a hollow opening inside a large tree.

During their exploration of Oneiros, the group periodically encounters Arche-Persona bosses at 20 floor intervals. The first 2 bosses depend on who the player has in his party upon reaching that floor. These first 2 bosses' stats are fixed and do not scale. Regardless, Fuuka and the Protagonist's Arche-Personas are always encountered on the 60th and 80th floors respectively.