This is a sequel to the first Ganbare Goemon Gaiden (side-story) RPG. Goemon, a cunning thief and an avid treasure hunting, has nothing to do and sits in his house, bored. But his trusty friend Ebisumaru has good news: there is a big treasure to find somewhere in a big city across the sea. Of course the treasure won't be just given to Goemon: he'll have to perform a dangerous mission before. The two friends board a ship and thus the journey begins...

The game is very similar to its predecessor, as well as to most other console-style RPGs of the period. You talk to people in towns, buy various equipment, descend into dungeons, and fight random enemies and bosses in turn-based combat. The combat perspective is slightly changed in this sequel (over-the-shoulder view of the battle instead of semi-animated pictures).