In London circa 1897, a young Scottish mouse named Olivia Flaversham is celebrating her birthday with her toymaker father, Hiram. Suddenly, Fidget, a bat with a crippled wing and a peg leg, bursts into the Flavershams' workshop, kidnapping Hiram. It is later revealed that Professor Padraic Ratigan kidnapped Hiram to create a clockwork robot which mimics the Queen of the Mice so Ratigan can rule England. Hiram refuses to take part in Ratigan's scheme, whereupon Ratigan orders Fidget to capture Olivia. If Hiram refuses to cooperate, Ratigan will have Olivia fed to his pet cat, Felicia.
Olivia searches to find Basil of Baker Street, a world-famous detective and Ratigan's archnemesis. Dr. David Q. Dawson stumbles upon Olivia, and helps her find Basil's residence. At first Basil is reluctant, but when Olivia mentions the peg-legged bat that kidnapped her father, Basil realizes that this is his chance to capture Ratigan. Basil and Dawson then use Sherlock Holmes' pet, a Basset Hound named Toby, to track Fidget's scent to a nearby toy store. Fidget is surprised by Basil, Dawson, and Olivia in the toyshop where he is stealing clockwork mechanisms and toy soldiers' uniforms for Ratigan's plan. He hides and later traps Olivia by ambushing her from inside a toy cradle. Basil and Dawson pursue Fidget but become entangled in some toys and fall behind, giving Fidget enough time to escape with all the materials he needs, along with Olivia.
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