Plot
In 1897 London, a young mouse named Olivia Flaversham celebrates her birthday with her single father, Mr. Flaversham, who is a gifted toymaker. A bat with a crippled wing and a peg leg arrives and kidnaps Flaversham. Olivia leaves to find Basil of Baker Street, the famous Great Mouse Detective. David Q. Dawson, a retired army surgeon mouse newly returned from Afghanistan, meets Olivia and escorts her to Basil's residence.
Basil initially dismisses them, but when Olivia mentions the bat that abducted her father, Basil realizes that Olivia saw Fidget, the assistant of Professor Ratigan, the criminal mastermind whom Basil was working to catch. It is then revealed that Ratigan kidnapped Flaversham to force him to create a clockwork robot replica of the Queen of the Mice, so that Ratigan can usurp her place as "Supreme Ruler of all Mousedom". Flaversham initially refuses to participate in the scheme, but capitulates when Ratigan threatens to harm Olivia.
Fidget appears in Basil's window, then suddenly disappears. Basil, Dawson and Olivia take Toby, Sherlock Holmes' pet Basset Hound, to trail Fidget's scent. They trace the bat to a human-sized toyshop. While searching the area, Dawson finds Fidget's checklist, and Basil discovers Fidget has been stealing clockwork mechanisms and toy soldiers' uniforms. Fidget ambushes and kidnaps Olivia before Basil and Dawson can stop him.
Basil conducts chemical tests to the checklist, discovering it came from the "Rat Trap", a tavern near the junction of the sewer and the Thames. Basil and Dawson disguise themselves as sailors and head to the tavern. They spot Fidget, and follow him to Ratigan's headquarters, only to be ambushed by Ratigan and his henchmen. Ratigan has the pair tied to a spring-loaded mousetrap connected to a Rube Goldberg machine of various killing devices. Ratigan then sets out for Buckingham Palace, where his henchmen hijack the royal guards' roles and kidnap the Mouse Queen. Inspired by a remark Dawson made, Basil deduces the trap's weakness, freeing himself, Dawson and Olivia.
At Buckingham Palace, Ratigan forces Flaversham to operate the toy Queen, while the real one is taken to be fed to Felicia, Ratigan's pet cat. The toy Queen declares Ratigan the ruler of all Mousedom, and he announces his dictatorial plans for his new "subjects". After Basil, Dawson, and Olivia save Flaversham and the real Queen, they restrain Fidget and Ratigan's other henchmen, while Toby chases Felicia until she jumps over a wall, into a pack of Royal Guard Dogs. Basil seizes control of the mechanical queen, making it denounce Ratigan as a fraud while breaking it into pieces. Realizing Ratigan's treason, the enraged crowd attacks, but Ratigan escapes on his dirigible with Fidget, holding Olivia hostage.
Basil, Dawson, and Flaversham create an airship from a matchbox, balloons, and a Union Jack, setting off in pursuit. Ratigan tosses Fidget overboard to lighten the load. Basil jumps onto the dirigible to confront Ratigan, causing it to crash straight into Big Ben's clockface. Inside the clocktower, Basil restrains Ratigan, rescues Olivia, and safely delivers her to Flaversham. Ratigan breaks free and attacks Basil, just before the clock strikes 10:00; the vibrations cause Ratigan to fall to his death. He attempts to take Basil with him, but Basil grabs a part of Ratigan's dirigible and saves himself.
Back at Baker Street, the group recounts their adventures. The Flavershams bid a fond farewell and leave to catch their train. Dawson reluctantly resolves to leave as well, until a new distressed client arrives. Basil introduces Dawson to her as his friend and investigative partner, prompting Dawson to remain and assist in Basil's future cases.