Ever since the Shredder mysteriously vanished following Kraang's attempted invasion, the Foot clan has been in disarray. With the help of Chief Vincent and the police force, the Ninja Turtles have been gradually hunting them down and bringing them to justice. But when a group of Foot soldiers flee to Japan, the Turtles pursue, and what they will find there will test all they know of themselves and will test Leonardo most of all, of where his loyalties lie.