The game is set in an alternate reality, in which Tokyo is invaded by hordes of demons. You play the role of a young man who lives in an underground shelter and is training to become a demon hunter with help of special programs. One day, during a training, one of the programs goes berserk, and as a result you are thrown into the world where you must fight for your life against vicious demons.
Giten Megami Tensei: Tokyo Mokushiroku is a non-canonical part of Megaten universe, featuring recurrent setting and story elements of the franchise. Like in classic Shin Megami Tensei games, the largest part of the game is spent in 3D dungeons, which are viewed from first-person perspective. The battle system introduces some unusual elements: enemies are visible before the actual battle begins, and during your dungeon exploration, you will be sometimes attacked from different sides. You will have to turn around to face the enemy in real time, but the game will be paused when you select commands from menu, in a traditional turn-based fashion.