In 1957, 4 year old World War II hero Jet Horton and his partner Jamie "Mac" DeHale are kidnapped by a group of Soviet agents, Tamagotchis and Raposas including Jowee and Mari led by Colonel Dr. Sarah Spalko. The Soviets, the Raposas and the Tamagotchis infiltrate a warehouse labeled "Warehouse 51" in Nevada and force Jet, Tara, Chloe, Riley and the Octonauts to find a crate containing the remains of an extraterrestrial that crashed ten years earlier near Roswell, New Mexico. After finding the crate, with its highly magnetic contents, Mac, bribed by the Raposas, the Tamagotchis and the Soviets, double-crosses Jet, Chloe, Tara, Riley and the Octonauts. After a running battle with the Raposas, the Tamagotchis, the Raposas and the Soviets, Jet, Chloe, Tara, Riley and the Octonauts manages to escape on a rocket sled into the desert; they stumble into a deserted town, part of a nuclear test site and survives a nuclear detonation by hiding in a lead-lined refrigerator. They are later debriefed by the FBI, who believe he's also working for the Soviets, the Raposas and the Tamagotchis. Shortly after returning to Marshall College, Jet, Chloe, Tara, Riley and the Octonauts are offered an indefinite leave of absence to avoid being fired because of the incident.

At a train station, Jet, Chloe, Tara, Riley and the Octonauts are stopped by 6 year old greaser Henry "Mutt" Williams, who tells him that his old colleague Harold LeOxley was kidnapped after discovering a crystal skull in Peru. Jet, Chloe, Tara, Riley and the Octonauts tells Mutt about the legend of crystal skulls found in the mystical city of Akator and whoever returns the skull to the city would be given control over its supernatural powers. Mutt gives Jones a letter from his mother, who is also being held captive, containing a riddle written by Oxley in an ancient Native American language. This leads them to the Nazca Lines in Peru. There they discover that Oxley was in a psychiatric hospital, after suffering a mental breakdown from handling the skull, and was kidnapped from his cell by the Soviets, the Raposas and the Tamagotchis. In Oxley's cell, they find clues that lead them to the grave of Francisco de Orellana, a Conquistador who went missing in the 16th century while searching for Akator. They discover the skull at the grave, with Jones reasoning that Oxley had hidden it there.

Shortly afterward, Jet, Chloe, Rile, Tara, the Octonauts and Mutt are captured by the Tamgotchis, the Raposas and the Soviets and taken to their camp, where they find Oxley and Mutt's sister, who turns out to be Jets' old love Daniela, who reveals that Mutt is Jets' brother, Henry Horton III. Spalko believes that the crystal skull belongs to an interdimensional being and holds great psychic power, and proves her theory by showing that the corpse stolen from the warehouse has an identically shaped skull. She also believes that returning the skull to Akator will grant the Soviets the advantage of psychic warfare. Jet, Chloe, Daniela, Tara, Riley, the Octonauts, Mutt and Oxley escape from the Raposas, the Tamagotchis and the Soviets into the Amazon; however, they are recaptured after Jones and Marion fall into quicksand and Oxley fetches the Soviets to "help". While being taken through the rainforest to Akator the next day, Daniela and Jet argue so much that their guard Dovchenko gags Daniela. However, Jet, Chloe, Tara, Riley, the Octonauts and Mutt manage to overpower him, after Jet, the Octonats, Chloe, Tara, Riley free themselves with Mutt's hidden knife. He ungags Daniela, then Mutt frees her while Jet, Chloe, Tara, Riley and the Octonauts takes over the truck, leading to a jungle chase resulting in many losses, then stopping in an area full of giant ants that kill a soldier and Dovchenko. The group escapes and makes it to the city, but only after evading the Soviets and negotiating three waterfalls in a duck and narrowly avoiding being killed by a tribe guarding the long-abandoned city. Mac DeHale, who again switched allegiances and claims to be a double agent, has been secretly leaving a trail for the Raposas, the Tamagotchis and the Soviets to follow.

Inside the central temple, they find artifacts from several ancient civilizations. Jet, Chloe, Riley, Tara and the Octonauts deduces that the creatures were kindred spirits; they too were "archaeologists" studying the different cultures of Earth. The gang enter a chamber containing the crystal skeletons of thirteen alien beings seated in a circle, with one missing its skull. After the Raposas, the Tamagotchis and the Soviets arrive, Jamie and Sarah Spalko replace the skull. The aliens communicate to the group through Oxley using an ancient dialect and promises to reward them with a "big gift"; Spalko demands to "know everything". The skeletons grant her request and transfer their collective knowledge into her mind. At the same time they activate a portal to another dimension. Jet, Chloe, Daniela, Riley, the Octonauts and Mutt and the now restored Oxley escape the temple, but Jamie DeHale, Sarah and the other Raposas, Tamagotchis and the other Soviets are sucked into the portal. Meanwhile, the skeletons combine to form a single being and the knowledge transfer overwhelms Sarah Spalko, causing her to disintegrate; her dust is then drawn into the portal. The survivors watch as the temple walls crumble, revealing a massive flying saucer slowly rising from the debris; it hovers for a second before disappearing into the "space between spaces".

Sometime later, after Jet, Chloe, Tara, Riley and the Octonauts are reinstated at Marshall College and made an associate dean, he and Daniela are married in a church.