The success of Indiana Jones and the Great Circle has shown that the future of the franchise once again might lie in video games, much like Indiana Jones and the Fate of Atlantis showed decades ago too. As such, the next step could be an adaptation one of the most beloved stories in the franchise. A new version could combine the original game's three separate paths and the comic into one definitive adventure, while following a structure similar to The Great Circle. The adaptation could also open with a prologue, similar to how The Great Circle opened with that of Raiders of the Lost Ark.
The story begins in 1912, where a young Indy discovers a group of grave robbers digging up the Cross of Coronado. After stealing the artifact and escaping across the desert and a circus train, Indy loses the Cross when he's forced to hand it over to the sheriff. It then cuts to 1939 to Barnett College, where the adult Indy finds the Cross again when looking for a horned statue at the behest of a Mr. Smith. After getting the statue however, Mr. Smith reveals himself to be Nazi agent Klaus Kerner and flees. In the following scuffle, Indy discovers Kerner is searching for Atlantis itself and his next target is Sophia Hapgood.
Indy travels to New York City to warn Sophia, an expert on Atlantis who studies a medallion connected to Atlantean king Nur-Ab-Sal. Together, they evade Kerner and meet Dr. Bjorn Heimdall, an Icelandic scholar who has been studying Plato's writings. Heimdall directs them to Azorean historian Felipe Costa, who has researched Plato's lost dialogue known as the Hermocrates. Costa reveals that a copy translated by archeologist Charles Steinhart was transferred to Hunter College. Indy and Sophia recover the copy, which reveals that Atlantis can only be reached by finding three stones.
Collecting the stones
The search for the first stone takes Indy and Sophia to Sternhart in Tikal, whom has already uncovered an Atlantean chamber beneath the ancient ruins. Inside the temple, the trio discovers the first stone -the Worldstone- hidden behind a series of traps. Sternhart attempts to claim the artifact for himself, but his actions activates one of the traps. As the traps are set in motion, Indy and Sophia escape with the Worldstone while Sternhart is trapped inside. With his dying breath, Sternhart shares the next stone is near Algiers. With that information, Indy and Sophia travel onward.
In Algiers, Indy and Sophia meet Omar Al-Jabbar, who reveals that the Nazis secretly have been searching for an Atlantean site beneath the Sahara. The pair travel to the excavation and discover another hidden temple. Before they can escape with the second stone -the Sunstone- Kerner and his soldiers arrive and take control of the situation. During the confrontation, the Nazis take the two stones and leave Indy and Sophia behind as the temple begins to collapse. After fleeing the site in an air balloon, Indy follows the Nazi trail to Monte Carlo to attempt to steal the stones back.
In Monte Carlo, Indy and Sophia discover that art scholar Alain Trottier has been targeted by Kerner because of his knowledge of Atlantis. After arriving in the city, Indy discovers Kerner wants Trottier to examine the stones for the next clue. Indy and Sophia infiltrate the party at which the exchange between Kerner and Trottier is set to take place. They are discovered and a chase ensues, but Indy and Sophia eventually do manage to retrieve Trottier and the stones. Trottier examines the Sunstone and shares that the final stone, the Moonstone, is locked beneath the ruins of Knossos in Greece.
Indy and Sophia travel to Knossos, where they discover the remains of an Atlantean colony hidden beneath the ancient palace. As they explore the underground ruins, they realize Kerner's men have already followed them there. After evading capture, Indy and Sophia discover the entrance to the Labyrinth. Using the Sunstone and the Moonstone, they activate an ancient mechanism that opens the entrance to the Labyrinth. After navigating the maze, they unlock a hidden map chamber that contains the third stone -the Wordstone- and shows that the path to Atlantis starts in Thera.
The final confrontation
Indy and Sophia travel to Thera to find the gateway to Atlantis. However, they are taken captive by Kerner. They descend toward the lost city in a submarine where they use the three stones to open the gateway. Suddenly, Sophia is targeted by Nur-Ab-Sal. Indy destroys the medallion and frees Sophia before continuing on toward the Colossus, a massive machine that once powered Atlantis. Kerner's attempts to control the ancient technology causes Atlantis to begin collapsing. Indy and Sophia escape aboard a secret subway as the legendary city disappears beneath the ocean once again.