In the year 1192, the darkness of the Minamoto clan has come and is spreading across Japan. The country is being ravaged, and only one man of the lost Heike clan can return from the depths of hell to put a stop to it. His name is Taira no Kagekiyo.
The story of Genpei Tōma Den ostensibly revolves around the historical Genpei War from Japanese history, and involves Taira no Kagekiyo fighting the evil Minamoto no Yoritomo and the Minamoto clan across Japan.
The game features three modes of play: "side mode", a small-scale action platforming section; "big mode", a large-scale fighting section comparable to the Taito coin-op Gladiator; and "flat mode", an overhead-view section. In all three sections the goal is to destroy enemies, collect items, and reach the end before the life bar (represented by burning candles) runs out.