While stopping the evil Dr. Wily once again, Mega Man finds himself trapped in a peaceful world populated by equines. With a new threat and an alliance looming on the horizon, Mega Man must find the Robot Masters and stop them.

But a lingering doubt lies within the Super Fighting Robot, making him wonder if he truly is a good hero. Can Mega Man put these aside with the help of his new friends and end Wily's plan to terrorize two worlds?

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?