The OSS has established a dedicated child spy division where siblings Carmen Cortez and Juni Cortez, portrayed by Alexa Vega and Daryl Sabara respectively, take on the exhilarating role of agents. Their parents, Gregorio Cortez and Ingrid Cortez, played by Antonio Banderas and Carla Gugino, are seasoned OSS spies themselves. As they navigate this new chapter, they find themselves in intense rivalry with the Giggles siblings, Gary and Gerti, the offspring of the duplicitous agent Donnagon Giggles.
The adventure kicks off at a local amusement park when the President's daughter, Alexandra, intentionally sabotages a thrilling ride to grab her father's attention, who frequently overlooks her. Amid the chaos, Carmen harbors a crush on Gary, complicating matters further. When the ride malfunction occurs, both the Cortez and Giggles children must rescue the passengers, leading to a showdown.
Meanwhile, the Cortez family is hopeful that Gregorio will ascend to the position of OSS Director at an upcoming award ceremony. However, in a shocking twist, Donnagon is announced as the new director instead, manipulating the teleprompter to ensure his victory. He rewards the Giggles kids for their apparent heroics, handing them level-one OSS badges, which frustrates the Cortez kids.
During the ceremony, the adults fall unconscious after indulging in wine that has been tampered with, leaving only the children free to act. Juni faces a setback when he's wrongfully blamed for losing the coveted "Transmooker," a device capable of shutting down all electronic devices. Determined to clear his name, Carmen hacks into the OSS's database to restore Juni's agent status, and together they embark on a perilous journey to an enigmatic island rumored to house exotic creatures.
As the subplot unfolds, they enlist the help of Fegan Flop and Minion, who confirm Donnagon's deceitful intentions. In his new role, Donnagon seeks to obtain the Transmooker to fulfill his sinister ambitions of global domination. Armed with their spy gadgets, Carmen and Juni utilize a submarine to reach the island. However, their vessel fails as they approach shore, forcing them to traverse the mysterious terrain equipped only in their underwater suits.
Back home, Gregorio and Ingrid, along with Ingrid's skilled parents, surge into action to locate their children, unaware of the dangers that lie ahead. Meanwhile, both sets of siblings endeavor to conquer the island's obstacles, only to discover they are utterly unarmed against the island's inherent dangers, including menacing creatures.
Their daring escapades bring them face-to-face with the eccentric scientist Romero, who is hell-bent on creating genetically modified creatures for profit. When they uncover Romero's true allegiance to Donnagon, the Cortez kids resolve to thwart the villain's plot before it spills over into chaos. They take a brave stance to destroy the Transmooker to prevent any possibility of annihilation.
The tension escalates as the Cortez parents activate a tracking device embedded in Juni's necklace, guiding them closer to their children's whereabouts. As the children inch closer to their goal, they engage in thrilling action sequences against terrifying foes, with Carmen ultimately changing her perception of Gary upon learning his true nature.
The climax sees the Cortez and Giggles communities banding together to combat Donnagon and reclaim the Transmooker, culminating in a ferocious battle. In a fitting conclusion, Donnagon is apprehended, leaving the Giggles family and their newfound alliances to celebrate their victory.
As the credits roll, a light-hearted twist unfolds where Machete instructs Carmen to perform as a budding pop star, utilizing clever gadgets to enhance her performance, only to reveal that she had been singing all along without any technical assistance, showcasing delightful comedic moments as their adventure concludes.
