After an accident from their most recent battle, Leonardo, Donatello, Raphael, Michaelangelo, and Master Splinter find themselves in a new world in the search of their nemesis, The Shredder.

Meanwhile, the Mane Six are called to Manehattan to investigate strange occurrences going on at night, bringing them into conflict with the Foot Clan. After a hasty escape, the turtles get discovered by the ponies after saving their lives.

After meeting, can the ponies and turtles stop Shredder? Or will two worlds fall in whatever he has planned?