Hubie and Marina's Adventures With Basil The Great Mouse Detective

In London, circa 1897, a young mouse named Olivia Flaversham is celebrating her birthday with her toymaker father, Hiram. Suddenly, Fidget, a bat with a peg leg, barges 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. Hiram initially refuses to participate in the scheme, but agrees when Ratigan threatens Olivia.

Returning to London after a tour of duty in Afghanistan, Dr. David Q. Dawson along with Hubie, Marina, Rocko, Petra, Beanie, Timmy, Pikatwo, Bonkers, Fawn and Buck stumble upon Olivia, who is searching for the renowned Basil of Baker Street. They escort Olivia to Basil’s residence and meet the detective. At first, Basil is reluctant, but when Olivia describes Fidget, Basil now realizes his chance to capture Ratigan. Basil, Dawson, Hubie and his friends take Toby, Sherlock Holmes's pet dog, to track Fidget's scent, where they find him in a toyshop stealing clockwork mechanisms and toy soldiers' uniforms. Fidget later traps Olivia and the bird kids by ambushing them from inside a toy cradle. Basil, Dawson, Hubie and the others pursue Fidget, but become entangled and fall behind. Basil blames Dawson for their capture, but soon apologises after Hubie and Marina scold him. The group discovers Fidget's checklist, to which Basil does some chemical tests to discover the list came from a riverfront near the Thames. Basil, Dawson, Hubie and their friends disguise themselves as sailors and go into a tavern called the "Rat Trap" and follow Fidget to Ratigan's headquarters. They are caught, and Ratigan ties them to a spring-loaded mousetrap connected with a Rube Goldberg machine. Ratigan sets out for Buckingham Palace, where Fidget and his accomplices kidnap the queen. Basil, along with Dawson, Hubie and the others deduce the trap's weakness and escape just in time.

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, Olivia, Hubie and all his friends save Hiram and the real Queen, and apprehend Fidget (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 defeating his guards. Ratigan frees himself and escapes on his dirigible with Fidget, holding Olivia and the birds hostage. Basil, Dawson, Hiram, Hubie, Marina and their friends create their own craft with a matchbox and some small helium-filled balloons, held together by the Union Jack. Ratigan had tied the bird kids up to make certain they don't fly away and tosses Fidget overboard to lighten the craft. He then attempts to drive the dirigible himself. Basil and Pikatwo jump on to the dirigible to confront Ratigan, causing him to crash straight into the Big Ben.

Inside the clock, Basil manages to get Ratigan's cape stuck on some gears and he and Pikatwo rescue Olivia and the birds and safely delivers them to Hiram and Hubie and his friends. Ratigan, however breaks free and attacks Basil and Pikatwo, eventually knocking them to the dirigible, until the clock bell strikes 10:00 and Ratigan falls to his death, taking Basil and Pikatwo with him. However, as Hubie and his friends mourn for Pikatwo, they notice Basil managed to grab the wreckage of Ratigan's dirigible and save both himself and Pikatwo from falling just in time.

Back at Baker Street, Basil and Dawson recount their adventures with Hubie and Marina and their friends, as well as the queen's gratitude for saving her life. Afterwards, the Flavershams leave to catch their train, and Hubie and his team say goodbye and leave for another adventure. As Dawson tries to leave, a distraught new client solicits Basil’s help, with Basil noting that Dawson is his trusted associate, prompting Dawson to remain and assist Basil.