This animated action adventure centres around Roddy St. James (Hugh Jackman), a decidedly upper crust pet rat who makes his home in a posh Kensington flat. While his owners are away on holiday Roddy plays around the house.
A common sewer rat named Sid (Shane Richie) comes spewing out of the sink and decides to stay, especially as England are playing against Germany in the World Cup final. Roddy schemes to get rid of Sid by luring him into the "jacuzzi", which is actually the toilet. Sid isn't fooled at all and instead pushes Roddy in and flushes him away into the sewer.
There, Roddy discovers a city resembling London made out of various bits of junk, and meets Rita Malone (Kate Winslet), an enterprising scavenger rat who works the drains in her faithful boat, the Jammy Dodger. Rita does not like Roddy initially, but ends up taking him along, while her arch enemy
The Toad (Ian McKellen) sends his rat henchmen, Spike (Andy Serkis) and Whitey (Bill Nighy), after her because she had stolen back her father's prized ruby a long time ago. The Toad despises all rodents to the point of hateful obsession. He plans to have them frozen with liquid nitrogen inside an icemaker. The pair escape, and Rita takes a unique electrical cable that, unknown to everyone but the Toad, is required to control the floodgates.
Roddy finds that the ruby is a fake and breaks it in front of Rita, enraging her, for she can now not get the money she needs for her large family. Roddy offers her a real ruby if she takes him back to Kensington. Accepting the offer, the pair first stop to visit her family before setting off.
During Roddy's stay, he overhears a conversation that causes him to think that Rita had double-crossed him, so he steals the Jammy Dodger. When Rita catches up to him, she is able to clear up the misunderstanding. The pair evade Spike and Whitey pursuing in a remote-controlled toy boat, with Thimblenose Ted and others on eggbeater jet skis. During this scene, Roddy and Rita share a quick love moment.
Incensed at his minions’ repeated failures, The Toad sends for his French cousin; an infamous, if somewhat laid back, mercenary known as Le Frog (Jean Reno). During this scene, it is revealed that The Toad was once Prince Charles' pet, but was replaced by a pet rat, and subsequently flushed down a toilet. Le Frog and his subordinates intercept the duo and retrieve the cable, but Roddy and Rita use a plastic bag to lift themselves out of the sewer (snatching away the cable during the ascent) and get Roddy home, though the Jammy Dodger is destroyed.
Back home, Roddy pays Rita the promised ruby and an emerald, then proceeds to show her around his house. She at first believes he has family in the home, but noticing his cage, she realises he's a pet. Roddy tries to pass Sid off as his brother, but Sid and Rita know each other. Rita tries to persuade Roddy to come with her, but he is too proud to admit that he is lonely.
By now, they have fallen in love but have not told each other their feelings. She departs, both of them broken-hearted, but is soon captured by The Toad. Talking to Sid about half-time, Roddy pieces together The Toad's plan: to open the gates during halftime of the World Cup, when all the humans will most likely be using their toilets, causing a great flood and drowning the rats and their underground city in sewage. He can then use the depopulated city as a home for his own tadpole offspring. He gives Sid his cushy position and has him flush him back to the sewers to find Rita and save the city.
Together, they defeat The Toad and freeze the wave of sewage generated by the flushing of countless toilets during half-time with liquid nitrogen before it drowns the entire rat population. Rita and Roddy build the Jammy Dodger Mark Two and set off in her with Rita's entire brood. A newspaper article reveals England had lost on penalties. Later while the credits start, Roddy's former owner Tabitha comes back with a new pet cat, which scares Sid.