(DOS version) Indiana Jones and the Fate of Atlantis is a puzzle-solving adventure game conceived in the spirit of Indiana Jones movies; however, it is not based on a specific movie, introducing a new, independent story. The game utilizes LucasArts' SCUMM system, with action verbs the player chooses from a menu; objects that can be interacted with are highlighted. The game contains many puzzles of various kinds (mostly inventory-based) and dialogues with multiple choices. There are also a few simple hand-to-hand fights against the Nazis, some of which can be avoided.
The middle part of the game can be played in three "modes": co-operation (Indy and Sophia), adventure (Indy alone), and action (Indy alone, with less puzzles and more action). In each mode there are different locations to visit, different puzzles to solve, and different characters to meet. The CD version of the game adds voice-overs to all the conversations.