Battle for Atlantis is a simple war game that pits a human player against 3 other computer controlled factions. The world is divided into regions on a host of islands. Each region can hold a number of troops and contributes to the faction's troop production each turn. As an entire island comes under the control of one faction, that faction's production increases significantly.

Random events may occur, including seismic activity, production booms, and so on, which shake up the game state for good or ill.

Battle for Atlantis plays much like Banyan Wars, though it features more colours, an update in AI and some slight gameplay changes.