After supervillain Shredder escapes custody, he joins forces with mad scientist Baxter Stockman and two dimwitted henchmen, Bebop and Rocksteady, to unleash a diabolical plan to take over the world. As the Turtles prepare to take on Shredder and his new crew, they find themselves facing an even greater evil with similar intentions: the notorious Krang.

After a construction project begins digging in their neighborhood, best friends Tuck, Munch and Alex inexplicably begin to receive strange, encoded messages on their cell phones. Convinced something bigger is going on, they go to their parents and the authorities. When everyone around them refuses to take the messages seriously, the three embark on a secret adventure to crack the code and follow it to its source. But taking matters into their own hands gets the trio in way over their heads when they discover a mysterious being from another world who desperately needs their help. The epic, suspenseful and exciting journey that follows will change all of their lives forever.