As Loid Forger receives news from Sylvia Sherwood, his handler at WISE, about his reassignment and replacement on "Operation Strix," an urgent sense of responsibility envelops him. Everything now hinges on his ability to make significant progress; however, it appears that his mission is already on shaky ground.
What ensues is a series of seemingly trivial interactions. Loid has a chat with fellow spy Fiona Frost, completely unaware that their conversation is being surveilled from a distance by his "wife," Yor Forger. This observation ignites Yor's imagination, prompting her to suspect that there's something romantic brewing between Loid and Fiona.
At the same time, Loid discovers from his "daughter," Anya Forger, that her class at Eden Academy is gearing up for a cooking competition, with the grand prize being a coveted Stella star. The judge, fond of a regional dessert called Meremere, presents Loid with an opportunity to reclaim the situation. With the judge being the principal who adores the dessert from Frigis, Loid sees a chance to turn the tides by recreating the delightful treat.
Their journey takes them to Frigis, where Anya stumbles upon a mysterious key. Utilizing her precognitive abilities, she taps into the mind of their pet Great Pyrenees, Bond Forger. This leads to a fateful discovery of a suitcase filled with chocolate, which Anya accidentally devours. Soon enough, the suitcase's owners come after them, but Yor steps in, effortlessly repelling their attempts to reclaim the suitcase.
Arriving at "Rubbles & Bonds" with the hope of indulging in their last Meremere, the atmosphere shifts dramatically when Colonel Snidel and his agents storm in, seizing the dessert for themselves. Defeated, Loid's spirits plummet further when he realizes that the restaurant's ingredients for recreating the beloved dessert have run dry.
Yor's anxiety about their relationship starts to surface, leading her to believe that Loid wants to end their marriage, despite receiving a thoughtful gift of lipstick from him. Her fears send her into a spiral of intoxication and public outbursts. Meanwhile, Anya, sensing the storm brewing between her parents through her unique abilities, orchestrates a chance encounter for them on a ferris wheel, allowing them to clear up their misunderstandings and reaffirm their bond.
However, the situation escalates when Snidel's plans for world domination take a bewildering turn. The chocolate Anya consumed harbors a tiny microfilm intended to instigate another war with Westalis, putting her directly in Snidel's crosshairs. While Loid frantically seeks out the last ingredient for the Meremere—cherry liquor—Anya steps up to use her powers to locate it and sneaks out, accompanied by Bond. They soon find themselves ambushed by Snidel's henchmen, resulting in Anya being captured, while Bond is left behind.
Back at the hotel, panic ensues as Loid and Yor search for any sign of Anya. Loid stumbles upon Bond, who provides crucial intel in the form of a military patch from their captors, leading him to deduce that Anya has been kidnapped. At that moment, Fiona arrives with urgent information from WISE, highlighting that the microfilm is of paramount importance. Loid, overhearing a military transmission, learns that Anya has ingested the incriminating film and realizes she’s being held aboard Snidel's airship. He resolves to take action, with Yor secretly opting to accompany him for assistance.
Tension escalates in a thrilling aerial dogfight as Snidel's airship launches guided missiles at Loid’s Bristol Beaufighter. Loid executes a daring crash landing on the airship, employing his disguise skills to slip past Snidel's guards. Meanwhile, Yor enters the fray, her guns blazing, accidentally igniting a fire that spreads wildly on the airship. Amidst the mayhem, Anya battles against a ticking clock, aware that Snidel intends to use her to retrieve the microfilm.
Remarkably, Anya finds a way to escape during Yor's rampage but is swiftly recaptured and hidden in the cockpit by Snidel. Unbeknownst to them, Loid has successfully disguised himself as a member of Snidel's crew, guided solely by his keen sense of smell. He finds himself in a showdown with Snidel, who instantly recognizes him due to his exceptional olfactory senses.
Displaying remarkable ingenuity, Anya manages to free herself just in time to open the windows, releasing the experimental gas intended for Loid. Seizing the opportunity, Loid performs a daring act, donning Snidel's outfit and commanding his crew to abandon ship. Meanwhile, Yor faces an intense battle against a formidable cyborg soldier known as Type F, emerging victoriously by transforming the lipstick Loid gifted her into a weapon against the machine.
The Forgers regroup, piloting their airship towards certain doom but ultimately manage to steer it into a river, narrowly avoiding a collision with the city. Amidst the chaos, Loid makes a vital discovery: the long-sought microfilm has lodged itself between Anya's teeth since their prior adventure. Upon returning home, he presents the precious microfilm to Sylvia, who expresses her satisfaction yet ensures that Operation Strix remains under his vigilant oversight.
Back at school, Anya prepares for her cooking competition with her peers, only for an unforeseen mishap to intervene, postponing the contest. The judge's sudden replacement with the vice principal gives Loid a fresh opportunity to propose another adventure, this time toward warmer locales in search of exquisite desserts. Bond’s precognitive insights assure him that this journey will serve as a much-needed escape from the typical chaos of the Forgers' lives.
In a post-credits scene, Franky Franklin arrives in Frigis, blissfully unaware that the Forgers have returned from their exploits, clutching a special gift—a bottle of cherry liquor meant for Loid.
