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 peg leg, bargses in, and after a brief struggle, disappears with Hiram. Fidget takes Hiram to Professor Ratigan, who commands him to create a clockwork robot, which mimics the Queen of the Mice so Ratigan can rule England. Among his notorious henchmen, Ratigan has also employed Heath Lynx, who agrees to serve Ratigan with promises of riches and glory. Hiram initially refuses to participate in the scheme, whereupon Ratigan threatens to harm Olivia.
Olivia searches to find Basil of Baker Street, a world-famous detective and Ratigan's archnemesis. Returning to London after a tour of duty in Afghanistan, Dr. David Q. Dawson stumbles upon Olivia, and helps her find Basil's residence. Along the way, they meet Logan and his crew, who had also arrived to London under mysterious circumstances and agree to help. At first, Basil is reluctant, but when Oliva mentions Fidget, Basil now realizes his chance to capture Ratigan. Basil and his friends take Toby, Sherlock Holme's pet dog, to track Fidget's scenet, where they find him in a toyshop stealing clockwork mechanisms and toy soldiers' uniforms. Fidget later traps Olivia by ambushing her from inside a toy cradle. Basil, Dawson, Logan, and his crew pursue Fidget, but become entangled and fall behind. While searching the shop, Dawson discovers Fidget's checklist, to which Basil does some chemical tests to discover the list came from a riverfront near the Thames. Basil, Dawson, Logan, and his crew disguise themselves as sailors (Logan and his crew using their Steampunk costumes) and go into a tavern called the "Rat Trap" and follow Fidget to Ratigan's headquarters. They are caught, Logan and his crew discover Heath's allegiance to Ratigan, who ties Basil and Dawson to a spring-loaded mousetrap connected with a Rube Goldberg machine, as Logan & his crew are bound to the roof and forced to watch. Ratigan sets out for Buckingham Palace, where Fidget and his accomplices kidnap the Queen. Basil, along with Dawson and their friends, deduce the trap's weakness and escape just in time.
Back at Buckingham Palace, Ratigan forces Hiram to operate the toy Queen, while the real Queen 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 tyrannical plans for his new "subjects". Just then, Basil, Dawson, Logan, his crew, and Olivia save Hiram and the real Queen, and apprehend Fidget and Heath (along with Ratigan's other henchmen). Basil seizes control of the mechanical queen, making it denounce Ratigan as a fraud and tyrant while breaking into pieces. The crowd, enraged by Ratigan's treason, start climbing on him and deafting his shanty guards (Meanwhile, Toby chases down Felicia and delivers her straight to the Royal Guard Dogs). Ratigan frees himself and escapes on his dirigible with Fidget and Heath, holding Olivia hostage. Basil, Dawson, and Hiram create their own craft with a matchbox and some small helium-filled balloons, held under the Union Jack, while Logan and his crew pilot The Trimaxian a.k.a. Max. Ratigan throws Fidget (Who can't fly) into the Thames River to his death, and then attempts to dive the dirigible himself. Basil, along with Logan and Justin, jumps on the dirigible to confront Ratigan, causing him to crash straight into the Big Ben. Inside the clock, Logan and Justin quickly remove Heath from the fight while Basil manages to get Ratigan's cape stuck on some gears and rescues Olivia and safely delivers her to Hiram. Ratigan, however breaks free and nearly kills Basil (even knocking him to the dirigible). Just as Ratigan is about to kill Logan and Justin, the clock bell strikes 10:00 and Ratigan falls to his death, taking Basil with him. However, Basil manages to grab the wreckage of Ratigan's dirigible and save himself from falling just in time.
Back at Baker Street, Basil, Dawson, Logan, and the crew recount their adventures, as well as the Queen's gratitude for saving her life. Afterwards, the Flavershams leave to catch their train while Logan and his friends return to their ship en route to their next big adventure. As Dawson tries to leave, a distraught new client persaudes both Basil and Dawson to help her. Finally, Basil proclaims Dawson to be his "trusted associate, Doctor Dawson, with whom I do all my cases".
- Miss Kitty (A singer with a small role in the movie) has an extended part.
- In this episode, The Council of Shadows recruit Rita Repulsa (At the very end).
- Heath Lynx makes a special guest appearance as Ratigan's henchman and meets Logan for the first time.
- Logan and the Crew use their "Steampunk" disguise from one of their earlier adventures.