The player controls an amateur adventurer named Wynn (ウィン), whose objective is to save his master being held captive in the final level.

Several years ago, a gigantic island arose from the southern Atlantic Ocean due to sudden shifts on the Earth's surface.

Armed with the special dynamite invented by the master, Wynn heads over to Atlantis all by himself to face an evil emperor who seeks to revive an ancient empire.

However, the somewhat choppy physics of Atlantis no Nazo, its one-hit deaths, and its multiple pathways make it much more challenging than Super Mario Bros.

The levels in the game are referred to as "zones", and the player travels through various locations such as fields, caves, ruins, temples, and even across clouds.

It would be one of the 30 games included on Nintendo's Classic Mini: Family Computer microconsole exclusively in Japan, released on November 10, 2016.