In the distant past of 6800 BC, a catastrophic explosion unleashes a megatsunami that devastates the city of Atlantis. In a desperate attempt to protect her people, the Queen merges with a floating crystal, creating an impenetrable dome over the city's core, shielding it from the impending disaster as the waves submerge Atlantis forever. The Queen's sacrifice leaves behind her husband, the King, and their courageous young daughter, Princess Kida.
Fast forward to 1914, where the passionate linguist Milo Thatch is on a quest to secure funding from the Smithsonian Institution for an expedition aimed at uncovering the mysteries of Atlantis. There, he encounters the quirky millionaire Preston B. Whitmore, an old friend of Milo’s late grandfather, Thaddeus. Encouraged by Whitmore, Milo eagerly joins the expedition and receives the Shepherd's Journal, an essential book that details the history and route to the fabled city. The expedition is led by the determined Commander Lyle Tiberius Rourke, accompanied by his devoted second-in-command Lieutenant Helga Sinclair, along with a diverse group: the demolition expert Vinny Santorini, the geologist Mole Molière, the compassionate medical officer Dr. Joshua Sweet, the skilled mechanic Audrey Ramirez, the radio operator Wilhelmina Packard, the humorous mess cook Cookie Farnsworth, and several brave soldiers.
As they delve deeper into their journey, the expedition’s submarine, Ulysses, comes face-to-face with a menacing mechanical leviathan guarding Atlantis's entrance, resulting in a catastrophic attack that decimates the crew. Following the journal’s guidance, the remaining team members navigate through a dormant volcano and finally arrive in Atlantis, where they are welcomed by the spirited and resilient Princess Kida.
Disregarding her father's explicit warnings, Kida seeks Milo's assistance in reclaiming the lost history of Atlantis, which has been deteriorating for centuries. As Milo delves into the heart of Atlantis, he uncovers the significance of a massive crystal known as the Heart of Atlantis, which bestows life and longevity upon its citizens and powers their technology through smaller crystals that they wear. He also realizes that Rourke, with ulterior motives, has been plotting to hijack the Heart all along. Feeling the grave threat, the Heart merges with Kida, further complicating the situation.
In a shocking turn of events, Rourke injures the King and confines Kida inside a crate, plotting their escape. However, Milo rallies his friends—Vinny, Audrey, Mole, Packard, Sweet, and Cookie—to defy Rourke and protect the Atlanteans from impending destruction. In a tense standoff, Rourke and Helga try to ascend to the surface with Kida, severing the bridge and cutting off the others. As the King imparts his final wisdom to Milo about the Heart's choice of a royal host in times of peril, he entrusts Milo with his own crystal, imploring him to save Atlantis and Kida, warning that she will forever remain lost to the crystal if they cannot separate her in time.
In a thrilling pursuit, Milo and his team inspire the Atlanteans to reactivate their ancient flying machines and confront the mercenaries. Rourke’s ruthless ambition leads to a violent confrontation with Helga, culminating in her tragic demise as she tries to thwart him. In the chaos over the Heart aboard a flaming airship, Milo unleashes a powerful shard of crystal, transforming Rourke into a crystalline statue, which is ultimately obliterated by the airship's blades. The perilous conflict ignites the volcano, forcing the heroes to return to Atlantis with Kida, who, still intertwined with the crystal, ascends into the sky and awakens the ancient Stone Guardians. These guardians valiantly raise the submerged parts of Atlantis, preserving the city from erupting lava. Once the danger subsides, the crystal miraculously restores Kida to life, reuniting her with Milo.
Opting to remain in Atlantis, Milo chooses to embrace a new life with Kida, having fallen deeply in love with her. Meanwhile, the expedition team returns to the surface with treasures and small Atlantean crystals, swearing to uphold the secrets of their adventures to safeguard Atlantis. Only Whitmore discovers the truth, piecing together the photographs captured by Mrs. Packard and the Atlantean crystal sent by Milo, revealing the incredible journey they embarked upon. In a poignant finale, Milo and the newly crowned Queen Kida share a serene moment as they orbit a stone effigy of her late father, while the Heart of Atlantis once more shines gloriously above the rejuvenated city.
