In Tokachi, Hokkaido, a young girl named Chie Yumi Adachi longs to see her mother, embryologist Naomi Ito, who moved to New York after divorcing Chie's paleontologist father, Akira Tsunehiko Watase. Akira and his assistant Daisuke Mitsuru Hirata are analyzing intriguing findings from a cave— a figurine of a child riding a Tyrannosaurus from the Jōmon period, both fossilized and non-fossilized eggs, and some cryptic writings. The researchers conclude that the inscriptions point to a language from Mu, the long-lost continent that once supposedly bridged myth and earth.
The next day, Chie joins Akira, Daisuke, and Fukutomi Masanobu Ando, a TV cameraman, on a renewed expedition into the cave. They encounter Shinoda Fujio Tsuneta, an elderly Ainu man who prays to the cave’s god before guiding them deeper inside. Their efforts lead them to an idol of a golden dinosaur and a mysterious translucent square pyramid containing a living secret, set before a column topped by a crystal skull. When Akira and Daisuke pick up the egg, the cave starts to cave in. Shinoda stays behind to soothe the deity and, before he ends his vigil, hands Chie an ocarina as the others scramble to safety.
Back at the laboratory, Fukutomi reveals Naomi has been invited to help hatch the extraordinary egg. Naomi arrives with clear ambivalence about reuniting with Chie, and Akira rebukes her for choosing work over family. Naomi attempts to transfer the egg’s nucleus into a sea turtle egg, but the substitute egg’s vitals falter. Yet when Chie plays the ocarina, the vital signs stabilize and the infant T. rex emerges—Rex—into the world.
Rex quickly becomes a national sensation after a televised debut. Chie teaches the hatchling to eat, to respond to a handful of words, and to master basic toilet habits. Through Daisuke, Rex signs up for a flurry of commercials, catapulting him into the spotlight. But the relentless schedule proves stressful, and Chie, Naomi, and Akira decide to free Rex from the contract so he can live more freely.
Time passes and Rex grows, while a plan to showcase him at a soon-to-be-built dinosaur museum takes shape. On Christmas Eve, Akira learns the museum director intends to claim Rex as a centerpiece. Chie and Rex flee once more, hoping to locate Rex’s biological kin. With help from a schoolfriend, they evade the director’s pursuit on snowmobiles and eventually escape in a hot air balloon. They find refuge in an igloo, and Shinoda arrives with Naomi and Akira, who have tracked them down. The group returns to the Mu temple ruins and discovers the remnants of an ancient Mu temple. In the distance, the Brocken spectre of Rex’s mother appears, and Chie and Rex share a poignant farewell as the young dinosaur heads toward its parent.
In a post-credits moment, Naomi seems to have returned to New York, leaving Chie with Akira and Sanae Ito Mitsuko Kusabue. Yet Naomi reappears, choosing to stay with them for good. With Fukutomi by their side, the family looks up to see a Rex-shaped cloud in the sky—a quiet, hopeful sign of Rex’s enduring bond with its family and with the ancient Mu world.
