The success of Indiana Jones and the Great Circle has shown that there is still plenty of interest for new Indiana Jones adventures. With that in mind, the next step could be a remake of Indiana Jones and the Fate of Atlantis, one of the franchise's most acclaimed stories outside of the films. A new version could combine the original game's three separate paths into one definitive adventure, while following the cinematic structure established by The Great Circle. The remake could also open with The Last Crusade's prologue, similar to how The Great Circle opened with Raiders of the Lost Ark's prologue.
The story begins in 1912, where a young Indy discovers the Cross of Coronado while investigating a group of grave robbers. After stealing the artifact and escaping across the desert and a circus train, Indy loses the Cross when the criminals catch up with him. 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 man calling himself Mr. Smith. However, Mr. Smith reveals himself to be Nazi agent Klaus Kerner and steals the horned statue. Indy then discovers Kerner is searching for Atlantis and Kerner's next target is Sophia Hapgood.
Indy travels to New York City to warn Sophia, who is an expert on Atlantis and studies a mysterious medallion connected to Atlantean king Nur-Ab-Sal. Together, they meet Dr. Bjorn Heimdall, a scholar who has been studying Plato's writings. Heimdall directs them to historian Felipe Costa, who has researched the lost dialogue known as the Hermocrates. Costa reveals that a copy translated by archeologist Charles Steinhart was actually transferred to Barnett College. Indy and Sophia recover the copy, which reveals that Atlantis can only be reached by finding the Worldstone, Sunstone and Moonstone.
Collecting the stones
The search for the first artifact takes Indy and Sophia to Tikal, where the archaeologist Charles Sternhart has already uncovered an Atlantean chamber beneath the ancient ruins. Inside the temple, Indy and Sophia discover the Worldstone hidden behind a series of ancient mechanisms. Sternhart attempts to claim the artifact for himself, but his actions activate a trap protecting the chamber. As the traps are set in motion, Indy and Sophia escape with the Worldstone while Sternhart is trapped inside and killed. With the first stone recovered, Indy and Sophia continue onward to Algiers.
In Algiers, Indy and Sophia meet Omar Al-Jabbar, who reveals that the Nazis have been searching for an Atlantean site beneath the Sahara. The pair travel to the excavation and discover another hidden temple containing the Sunstone. Before they can escape with the artifact, Kerner and his soldiers arrive and take control of the situation. During the confrontation, the Nazis take the Sunstone 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 Sunstone 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 discover Kerner intends to have Trottier examine the Sunstone for the next clue. Indy and Sophia infiltrate the party at which the exchange between Kerner and Trottier is set to take place. They slip past Kerner's men, steal the artifact back and escape with Trottier. As thanks, Trottier examines the Sunstone and shares that the final artifact, 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 discover the Cult of Mithras is there to investigate Theseus' defeat of the Minotaur. After evading capture, Indy and Sophia discover a hidden chamber containing the entrance to the Labyrinth. They activate an ancient mechanism that opens the entrance to the Labyrinth. After navigating the maze, they recover the Moonstone and discover a hidden map chamber that shows the path to Atlantis starts in Thera.
The final confrontation
Indy and Sophia travel to Thera and use the three stones to open the gateway to Atlantis. However, they are followed by Kerner and taken captive. They descend toward the lost city in a submarine, where Sophia is targeted by Nur-Ab-Sal in an attempt to return to power. Indy destroys the medallion and frees Sophia before confronting the Nazis at the Colossus, the 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 elevator as the legendary city disappears beneath the ocean once again.