When you are in the dark, the normal "Look" command is automatically replaced with a "Touch" command. Click on Sophia for hilarious responses.
After finding Plato's Lost Dialogue, the player is given the chance to pursue one of three mutually exclusive paths, which have been nicknamed "Wits" (more emphasis on puzzles), "Fists" (more combat encounters) and "Team" (Indy continues the adventure with Sophia). Based on previous choices made, Sophia will suggest one of the three, but the player is free to choose. The three paths have unique storylines that eventually converge at Atlantis during the last act of the game. Co-writer/director Noah Falstein said that these branching storylines were created in response to feedback to Indiana Jones and the Last Crusade: The Graphic Adventure (1989); due to certain elements appealing differently to different players, Fate of Atlantis was made to please casual gamers who were satisfied with finishing their preferred path in 10 to 12 hours, yet also appeal to the completionists who would also want to finish the other two paths. A feature called the "Indy Quotient" (lifted from The Last Crusade) was implemented to keep track of all the puzzles solved, and enable players to identify all the different variations in the game.
The shelf in Indy's office features Easter eggs:
- A cartouche from the Well of Souls from Raiders of the Lost Ark (1981),
- A Thugee idol from Indiana Jones and the Temple of Doom (1984),
- A purple glowing meteor that won't stop glowing, from Maniac Mansion (1987) (another LucasArts adventure game),
- and letters from Indy's dad to the school board, which all start off with "Regarding Henry", reffering to the drama film Regarding Henry (1991), which starred Indiana Jones film actor Harrison Ford.
One of the items Omar offers is a baseball he claims is signed by Lou Gehrig, but when Indy examines it he says, "It's signed by some guy named Ron Gilbert". Ron Gilbert is the creator of the Maniac Mansion and Monkey Island series, as well as the SCUMM game engine which most LucasArts adventure games use.
There are references in the game to every Indiana Jones film made at the time of the game's creation:
- Raiders of the Lost Ark (1981) - On the shelf in Indy's office is a cartouche from the Well of Souls. At the Algerian dig site, there is a depiction of the Ark of the Covenant from on one of the walls (Indy aptly remarks that he has seen that before). The labyrinth on Crete features a giant boulder trap.
- Indiana Jones and the Temple of Doom (1984) - On the shelf in Indy's office at Barnett College, their is a Thugee idol.
- Indiana Jones and the Last Crusade (1989) - In one of the Atlantean chambers, there is a stone cup to which Indy remarks that it is definitely not the cup of a carpenter, a reference to the Holy Grail. There is also a "X marks the spot" on Crete.