Roddy St. James is no ordinary rat; he is a pampered pet living in a luxurious Kensington apartment. However, his life takes an unexpected turn when, one fateful night, a sewer rat named Sid emerges from the sink's drain to watch the thrilling 2006 FIFA World Cup Final. In a bid to reclaim his space, Roddy tries to flush Sid down the Jacuzzi brand toilet, deceitfully claiming it to be an actual jacuzzi. The plan backfires when Sid turns the tables and flushes Roddy instead.
Roddy's journey leads him to Ratropolis, a chaotic and cleverly constructed sewer city resembling London. Here, he learns about Rita Malone, a resourceful scavenger who navigates the drains using her trusty boat, the Jammy Dodger. She might just be the ally Roddy needs to find his way back home. Unfortunately, the duo finds themselves captured by the henchmen, Spike and Whitey, and brought before their ruthless boss, the Toad. The Toad has a sinister plan, wishing to freeze Roddy and Rita using liquid nitrogen, as he seeks revenge for a prized ruby stolen by Rita that belonged to her father.
As fate would have it, Roddy uncovers that the ruby is merely a fake and shatters it, which infuriates Rita. In an attempt to make amends, Roddy promises a genuine ruby if she returns him to Kensington. They make a pit stop to visit Rita’s family, but after overhearing a conversation, Roddy mistakenly suspects Rita of betraying him to the Toad. Acting out of pride, he steals the Jammy Dodger and runs away, only for Rita to catch up and clarify the misunderstanding. Together, they evade the relentless pursuit of Spike, Whitey, and their goons.
Angered by the consistent failures of his minions, the Toad calls upon his French cousin, Le Frog. This revelation unveils the Toad’s dark past: he was once Prince Charles' treasured pet before being unceremoniously replaced and flushed down a toilet, fueling his loathing for all rodents. When Le Frog and his accomplices try to retrieve the crucial cable from Roddy and Rita, the duo narrowly escapes, although the Jammy Dodger meets a tragic end.
Back at Roddy's apartment, he offers Rita the promised ruby, along with an emerald, and gives her a tour of his lavish home. Initially, she believes he has a family, only to discover his cage, leading her to realize his loneliness. Despite Rita’s urging to join her, Roddy’s pride prevents him from admitting how alone he truly feels. Just as she leaves through the toilet, disaster strikes when the Toad kidnaps her and takes back the essential cable.
Seizing the moment, Roddy teams up with Sid to strategize against the Toad’s nefarious plan. With half-time approaching in the World Cup, he deduces that the Toad intends to unleash a catastrophic flood during this time, aiming to wipe out Ratropolis and make it a breeding ground for his tadpole offspring. Putting his faith in Sid's strength, Roddy decides to take the plunge back into the sewers to save Rita. Together, they confront the Toad and his henchmen, outsmarting them by trapping their tongues in the gears and utilizing liquid nitrogen to freeze the oncoming wave.
Celebrated as a hero, Roddy opts to remain in Ratropolis alongside Rita. In a heartwarming conclusion, the pair, along with Rita's family, embark on a new adventure onboard the Jammy Dodger II.
In a humorous mid-credits scene, Sid enjoys his newfound comfort in Kensington. However, his luck quickly turns as Tabitha, Roddy's owners' daughter, discovers him lounging on the couch, introducing him to their new cat with a hint of horror.
