Fate of Atlantis is based on the SCUMM story system by Ron Gilbert, Aric Wilmunder, Brad P. Taylor, and Vince Lee, thus employing similar gameplay to other point-and-click adventures developed by LucasArts in the 1980s and 1990s. The player explores the game's static environments while interacting with sprite-based characters and objects; they may use the pointer to construct and give commands with a number of predetermined verbs such as "Pick up", "Use" and "Talk to". Conversations with non-playable characters unfold in a series of selectable questions and answers.
Early on, the player is given the choice between three different game modes, each with unique cutscenes, puzzles to solve and locations to visit: the Team Path, the Wits Path, and the Fists Path. In the Team Path, protagonist Indiana Jones is joined by his partner Sophia Hapgood who will provide support throughout the game. The Wits Path features an abundance of complex puzzles, while the Fists Path focuses heavily on action sequences and fist fighting, the latter of which is completely optional in the other two modes. Atypical for LucasArts titles, it is possible for the player character to die at certain points in the game, though dangerous situations were designed to be easily recognizable. A score system, the Indy Quotient Points, keeps track of the puzzles solved, the obstacles overcome and the important objects found.
Plot
The story of Fate of Atlantis is set in 1939, on the eve of World War II. At the request of a visitor named Mr. Smith, archaeology professor and adventurer Indiana Jones tries to find a small statue in the archives of his workplace Barnett College. After Indy retrieves the horned figurine, Smith uses a key to open it, revealing a sparkling metal bead inside. Smith then pulls out a gun and escapes with the two artifacts, but loses his coat in the process. The identity card inside reveals "Smith" to be Klaus Kerner, a Nazi agent. Also inside the coat is an old magazine containing an article about an expedition on which Jones collaborated with a young woman named Sophia Hapgood, who has since given up archaeology to become a psychic.
Fearing that she might be Kerner's next target, Indy travels to New York City to warn her and to find out more about the mysterious statue. There, he interrupts her lecture on the culture and downfall of Atlantis, and the two return to Sophia's apartment. They discover that Kerner ransacked her office in search of Atlantean artifacts, but Sophia says that she keeps her most valuable item, her necklace, with her. She owns another of the shiny beads, now identified as the mystical metal orichalcum, and places it in the medallion's mouth, invoking the spirit of the Atlantean king Nur-Ab-Sal. She explains that a Nazi scientist, Dr. Hans Ubermann, is searching for the power of Atlantis to use it as an energy source for warfare.
Sophia then gets a telepathic message from Nur-Ab-Sal, instructing them to find the Lost Dialogue of Plato, the Hermocrates, a book that will guide them to the city. After gathering information, Indy and Sophia eventually find it in a collection of Barnett College. Correcting Plato's "tenfold error", a mistranslation from Egyptian to Greek, the document pinpoints the location of Atlantis in the Mediterranean, 300 miles from the Kingdom of Greece, instead of 3000 as mentioned in the dialogue Critias. It also says that in order to gain access to the Lost City and its colonies, three special engraved stones are required. At this point, the player has to choose between the Team, Wits, or Fists path, which influences the way the stones are acquired. In all three paths, Jones meets an artifact dealer in Monte Carlo, ventures to an archaeological dig in Algiers, explores an Atlantean labyrinth in Knossos on Crete, and Sophia gets captured by the Nazis. Other locations include the remains of a small Atlantean colony on Thera, a hydrogen balloon and a Nazi submarine.
The individual scenarios converge at this point as Indiana makes his way to the underwater entrance of Atlantis near Thera and starts to explore the Lost City. He figures out how to use various Atlantean devices and even produce orichalcum beads. With this knowledge he saves Sophia from a prison, and they make their way to the center of Atlantis, where her medallion guides them to the home of Nur-Ab-Sal. The spirit of the Atlantean king takes full possession of Sophia and it is only by a trick that Indy rids her of the necklace and destroys it, thus freeing her. Meanwhile, they notice grotesquely deformed bones all over the place. They advance further and eventually reach a large colossus the inhabitants of the city built trying to transform themselves into gods. They had hoped using ten orichalcum beads at a time would enable them to control the water with the powers they gained, keeping the sea level down to prevent an impending catastrophe.
Unknowingly, Indiana starts the machine, upon which Kerner, Ubermann, and Nazi troops invade the place and announce their intention to use the machine to become gods. The machine was responsible for creating the mutated skeletons seen earlier, but the Nazis believe that it will work on them due to their Aryan qualities. Kerner insists to step onto the platform first, claiming himself to be most suitable for godhood. After Jones mentions Plato's tenfold error, Kerner decides to use one bead instead of ten. He is turned into a horribly deformed and horned creature, and jumps into the surrounding lava. Indiana is forced to step on the platform next but threatens Ubermann with eternal damnation once he is a god. Fearing his wrath, Ubermann uses the machine on himself, feeding it one hundred beads. He is turned into a green ethereal being, but his form becomes unstable and he flies apart with an agonized scream.
Two alternative bad endings see one of the protagonists undergo the second transformation if Indiana could not convince Ubermann to use the machine instead, or if Sophia was not freed from her prison and Nur-Ab-Sal's influence. In the happy ending, Atlantis succumbs to the eruption of the still active volcano as the duo flees from the city. The final scene depicts Indiana kissing Sophia on top of the escape submarine, to comfort himself for the lack of evidence for their discovery.
