In the mysterious fog of 1897 London, a lively young mouse named Olivia Flaversham joyously celebrates her birthday alongside her single father, the talented toymaker Mr. Flaversham. However, their cheerful day takes a dark turn when a bat with a worn wing and a peg leg suddenly swoops in, abducting Olivia’s beloved father. Undaunted, Olivia embarks on a dangerous quest to seek assistance from the famed Great Mouse Detective, Basil, but she soon finds herself lost in the winding, unfamiliar streets of London. In her journey, she crosses paths with David Q. Dawson, a retired army surgeon mouse who has just returned from service in Afghanistan. Dawson, with his kindhearted nature, offers to help Olivia reach the celebrated detective.
Initially, Basil is too wrapped up in his own interests to lend an ear to the urgent pleas of Olivia and Dawson, brushing them off with a dismissive wave. The situation changes drastically when Olivia mentions the strange bat that stole her father—revealed to be Fidget, the loyal accomplice of the infamous Professor Ratigan, a villain that Basil has been earnestly pursuing. Understanding the gravity of the situation, Basil realizes that Ratigan has sinister plans for Mr. Flaversham, intending to create a mechanical replica of the revered Mouse Queen to seize the throne of Mousedom for himself. Despite his initial hesitation, Mr. Flaversham is forced to comply with Ratigan's demands under the threat to his beloved Olivia.
As the adventure unfolds, Fidget unexpectedly appears at Basil's window, only to inexplicably vanish, pushing Basil, Dawson, and Olivia to follow his trail. Their investigation leads them to a toy shop filled with random clockwork parts and toy soldiers’ attire. During their search, Dawson stumbles upon Fidget's meticulously kept checklist, while Basil discovers a treacherous plan that involves stealing essential parts for Ratigan’s malevolent scheme.
When Fidget launches a sudden attack and captures Olivia, Basil and Dawson remain resolute to rescue her. Employing his keen deductive skills, Basil traces Fidget's checklist back to the notorious "Rat Trap" tavern along the Thames. Disguising themselves as sailors, the duo infiltrates the tavern and follows Fidget to Ratigan's hideout. However, things quickly spiral out of control as they are ambushed by Ratigan and his henchmen.
In a twist of fate, Basil, Dawson, and Olivia find themselves trapped in a perilous and convoluted mousetrap linked to a ferocious Rube Goldberg machine filled with lethal contraptions—all while the real Mouse Queen is held captive, awaiting a terrible fate in Buckingham Palace. But with a spark of inspiration from Dawson, Basil is able to identify the trap’s weakness and manages to escape along with his companions.
Meanwhile, at Buckingham Palace, Ratigan forces Mr. Flaversham to manipulate the mechanical Queen, while the true ruler faces a dreadful threat from Felicia, Ratigan's clever feline companion. As the clockwork Queen declares Ratigan the ruler of Mousedom, Basil and his allies spring into action, rescuing both Mr. Flaversham and the real Queen. They confront Fidget and Ratigan's other henchmen, leading to a chaotic chase that sends Felicia tumbling away from danger thanks to the intervention of Toby, a dog on their side. Ultimately, Basil captures the mechanical Queen just as it denounces Ratigan, leading to chaos as the onlookers realize his treachery.
However, Ratigan escapes with Fidget and Olivia aboard his airship, forcing Basil, Dawson, and Mr. Flaversham to construct their own makeshift airship from simple materials—a matchbox, balloons, and a Union Jack. They pursue Ratigan through the skies, resulting in an epic confrontation that sees Basil leaping aboard Ratigan's dirigible as it spirals towards the iconic Big Ben. A fierce battle ensues inside the clock tower, where Basil outmatches Ratigan, liberating Olivia and ensuring her safe reunion with her father. In a final showdown, Ratigan's hubris leads to his downfall as he tries to attack Basil; ultimately, the ticking clock spells his doom as the vibrations from the clock's chime send him plummeting to defeat.
Upon their triumphant return to Baker Street, the trio excitedly recount their adventures. The Flavershams say their goodbyes, and although Dawson considers leaving, a new case arises, prompting Basil to introduce Dawson as his trusted partner. This moment solidifies Dawson's decision to stay, ready to tackle future mysteries by Basil's side.
