Leonardo returns from Japan to find the lair in ruins and his family nowhere to be seen. As he investigates he finds that the Foot is back to full strength - with Karai as their leader. Since the Foot believe Leo to be dead, he puts all that he has learnt from the Anicent One into practice...

For several years April's uncle Augustus (aka Augie) has been missing. One day she gets a message from him via the mysterious artifact last seen in season 2 "April's Artifact", and April and Donatello has to go too another dimension and save him.