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 Indiana retrieved 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 he loses his coat in the process. The identity card inside reveals "Smith" to be Klaus Kerner, an agent of the Third Reich. Another pocket of the coat holds an old magazine containing an article about an expedition on which Indiana collaborated with Sophia Hapgood, who has since given up archeology to become a psychic. Fearing that she might be Kerner's next target, Indiana travels to New York in order 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 god Nur-Ab-Sal. She explains that a Nazi scientist called Dr. Hans Ubermann is searching for the power of Atlantis to use it as an energy source for warfare.
A video game screenshot showing the two protagonists in the middle of a crowded marketplace. The lower part of the image shows a variety of objects on the right side and a number of verbs such as "Pick up", "Use" and "Talk to" on the left side. The mouse cursor is pointing at Sophia, making the current command "Talk to Sophia".
Indiana and Sophia in an Algerian marketplace. Below the scene the game displays the core of the SCUMM system, the verbs and objects that the player may construct commands with.
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, Indiana 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 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 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, Sophia gets captured by the Nazis, and Indiana makes his way to the underwater entrance of Atlantis near Thera.
The individual scenarios converge at this point and Indiana starts to explore the Lost City. 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 Atlantean god takes full possession of Sophia and it is only by a trick that Indiana rids her of the necklace and destroys it, thus freeing her. They advance further and eventually reach a large colossus the inhabitants of the city built to transform themselves into gods. 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 with the stones, upon which Kerner, Ubermann, and the Nazi troops invade the place. Ubermann wants to use Indiana as a test subject, but Kerner steps onto the platform first, claiming himself to be most suitable for godhood. Just as Ubermann wants to start the machine, Indiana mentions Plato's tenfold error, which convinces Kerner to use one bead instead of ten. He is then turned into a horribly deformed and horned creature, and falls into the lava. Indiana is forced to step on the platform next but threatens Ubermann to send him straight to hell 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 before vanishing completely. Three 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 or Nur-Ab-Sal's influence. In the good 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.By: binford6001