The prophet Nostradamus has foreseen that the world as we know it shall end in the year 1999, and the thousand-year kingdom of angels and children will commence. A young boy named Shou is at first unaware of these prophecies, enjoying a normal life with his sweetheart Alisa. However, a series of events changes his life forever, as he is entrusted with the task of saving humans by discovering the ancient continent of Atlantis.

1000-nen ?koku is an adventure game viewed from first-person perspective. Navigation and interaction with the environment is performed by selecting verb commands from a menu and combining them with objects selected from a list. Though the game largely follows a puzzle-less Japanese format, the commands include (beside the traditional "Examine", "Talk", and "Move") options such as "Take" and "Buy", requiring interaction with items.