After the defeat of their old arch nemesis, The Shredder, the Turtles have grown apart as a family. Struggling to keep them together, their rat sensei, Splinter, becomes worried when strange things begin to brew in New York City.

Alice, an unpretentious and individual 19-year-old, is betrothed to a dunce of an English nobleman. At her engagement party, she escapes the crowd to consider whether to go through with the marriage and falls down a hole in the garden after spotting an unusual rabbit. Arriving in a strange and surreal place called ‘Underland,’ she finds herself in a world that resembles the nightmares she had as a child, filled with talking animals, villainous queens and knights, and frumious bandersnatches. Alice realizes that she is there for a reason – to conquer the horrific Jabberwocky and restore the rightful queen to her throne.

A team of trained secret agent animals, guinea pigs Darwin, Juarez, Blaster, mole Speckles, and fly Mooch takes on a mission for the US government to stop evil Leonard Saber, who plans to destroy the world with household appliances. But the government shuts them down and they are sentenced to a pet shop. Can they escape to defeat the villain and save the world?